>CHA349 (CHA349Q) /CSM/CH/CHA3-C/CHA349Q.Seq.d/
AATTTACAATAATAACAAAGATGACAAGCAATACAACTGAAATACCCTATCATTTTTTAC
CATATGTAAGAATTCAATATGATTGGCAATTGGCATATAAACAAGATTCAGATAATTGTT
GGGTTGCATATCAAAAAGATTTAAAAAATACAATTCATGGATCAGTTCATTCTACCAAAA
TTGATGAAAATAATTTTAAATTTGAATCTGATTATGGATTTAAATTAACACCAAATAAAG
AAAATAAAAATAATATTAGAGTTGAAAATGATAAATATAGTATTGAAATATATGCACCAG
AGAAACAGTTAAAAGTTTCAGGTGGAAAGAAAAGAATAACATCAATGGGTGTTAGTCATT
TAGGAGAGTTGGGTGTATATGGTAGTACTGATGGTACATTGGAAGTATTTGAAACTGGTG
ATGGTCAAATTAGAAGAAAATTAGATGGTCATGTTGGTGATGTTGATTTGGCAATGTTTT
TCCCAAGTGGTAGGGTTATACTAAGTGGTTCCTCTGATAGTAGATTAAAGATTTGGGATG
CTATAGAAGGCACATGCGXXXXXXXXXX

FTIITKMTSNTTEIPYHFLPYVRIQYDWQLAYKQDSDNCWVAYQKDLKNTIHGSVHSTKI
DENNFKFESDYGFKLTPNKENKNNIRVENDKYSIEIYAPEKQLKVSGGKKRITSMGVSHL
GELGVYGSTDGTLEVFETGDGQIRRKLDGHVGDVDLAMFFPSGRVILSGSSDSRLKIWDA
IEGTC---

Frame A:
nlq**qr*qaiqlkypiifyhm*efnmignwhinkiqiivglhikki*kiqfmdqfilpk
lmkiilnlnlimdln*hqikkikiilelkminivlkymhqrns*kfqverke*hqwvlvi
*eswvymvvlmvhwkylklvmvkleen*mvmlvmliwqcfsqvvgly*vvplivd*rfgm
l*kah---


Frame B:
iynnnkddkqyn*ntlsffticknsi*laigi*trfr*llgciskrfkkynswissfyqn
**k*f*i*i*lwi*intk*rk*k*y*s*k**i*y*nictretvksfrwkeknningc*sf
rrvgciw*y*wyigsi*nw*wsn*kkirwscw*c*fgnvfpkw*gytkwfl***ikdlgc
yrrhm---


Frame C:
FTIITKMTSNTTEIPYHFLPYVRIQYDWQLAYKQDSDNCWVAYQKDLKNTIHGSVHSTKI
DENNFKFESDYGFKLTPNKENKNNIRVENDKYSIEIYAPEKQLKVSGGKKRITSMGVSHL
GELGVYGSTDGTLEVFETGDGQIRRKLDGHVGDVDLAMFFPSGRVILSGSSDSRLKIWDA
IEGTC---

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VFF547 (VFF547Q) /CSM/VF/VFF5-B/VFF547Q.Seq.d/                       1106   0.0
CHE313 (CHE313Q) /CSM/CH/CHE3-A/CHE313Q.Seq.d/                       1106   0.0
CHE165 (CHE165Q) /CSM/CH/CHE1-C/CHE165Q.Seq.d/                       1106   0.0
CHA349 (CHA349Q) /CSM/CH/CHA3-C/CHA349Q.Seq.d/                       1106   0.0
CFI320 (CFI320Q) /CSM/CF/CFI3-A/CFI320Q.Seq.d/                       1106   0.0
CFH720 (CFH720Q) /CSM/CF/CFH7-A/CFH720Q.Seq.d/                       1106   0.0
CFH514 (CFH514Q) /CSM/CF/CFH5-A/CFH514Q.Seq.d/                       1106   0.0
CFC387 (CFC387Q) /CSM/CF/CFC3-D/CFC387Q.Seq.d/                       1106   0.0
CFC339 (CFC339Q) /CSM/CF/CFC3-B/CFC339Q.Seq.d/                       1106   0.0
AFF810 (AFF810Q) /CSM/AF/AFF8-A/AFF810Q.Seq.d/                       1106   0.0

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

AC117081|AC117081.2 Dictyostelium discoideum chromosome 2 map 5862124-6045772 strain AX4, complete sequence.   632   0.0    11
AC116920|AC116920.3 Dictyostelium discoideum chromosome 2 map 4415041-4520361 strain AX4, complete sequence.    42   1e-08  12
AL844507|AL844507.1 Plasmodium falciparum chromosome 8.            36   3e-08  20
AC116979|AC116979.3 Dictyostelium discoideum chromosome 2 map 6445720-6776760 strain AX4, complete sequence.    36   3e-07  18
AC116984|AC116984.2 Dictyostelium discoideum chromosome 2 map 2567470-3108875 strain AX4, complete sequence.    44   4e-07  16
AL929354|AL929354.1 Plasmodium falciparum strain 3D7, chromosome 5, segment 4/4.    40   5e-07  12
AE014829|AE014829.1 Plasmodium falciparum 3D7 chromosome 10 section 1 of 7 of the complete sequence.    32   8e-07  16
AE017263|AE017263.1 Mesoplasma florum L1 complete genome.          38   1e-06  20
AC116986|AC116986.2 Dictyostelium discoideum chromosome 2 map 2234041-2567370 strain AX4, complete sequence.    36   4e-06  14
AP006628|AP006628.1 Onion yellows phytoplasma OY-M DNA, complete genome.    36   5e-06  18

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q8MYE8) RecName: Full=Probable proteasomal ATPase-associated fa...   372   e-102
AK222501_1(AK222501|pid:none) Homo sapiens mRNA for hypothetical...   101   1e-20
BC006142_1(BC006142|pid:none) Homo sapiens proteasomal ATPase-as...   101   1e-20
(Q5ZK69) RecName: Full=Proteasomal ATPase-associated factor 1; A...   100   3e-20
AB171255_1(AB171255|pid:none) Macaca fascicularis brain cDNA clo...    99   7e-20
(Q148I1) RecName: Full=Proteasomal ATPase-associated factor 1; A...    98   1e-19
BC070729_1(BC070729|pid:none) Xenopus laevis hypothetical protei...    89   6e-17
AF087895_1(AF087895|pid:none) Homo sapiens G-16 mRNA, complete c...    87   2e-16
BC028628_1(BC028628|pid:none) Homo sapiens proteasomal ATPase-as...    87   2e-16
BC088671_1(BC088671|pid:none) Xenopus laevis cDNA clone MGC:9909...    87   4e-16

 psg: 0.73  gvh: 0.24  alm: 0.43  top: 0.53  tms: 0.00  mit: 0.31  mip: 0.05
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 40.0 %: nuclear
	 28.0 %: cytoplasmic
	 12.0 %: mitochondrial
	  8.0 %: plasma membrane
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: peroxisomal

>> prediction for CHA349 is nuc

>CHA349F.Seq
AATTTACAATAATAACAAAGATGACAAGCAATACAACTGAAATACCCTATCATTTTTTAC
CATATGTAAGAATTCAATATGATTGGCAATTGGCATATAAACAAGATTCAGATAATTGTT
GGGTTGCATATCAAAAAGATTTAAAAAATACAATTCATGGATCAGTTCATTCTACCAAAA
TTGATGAAAATAATTTTAAATTTGAATCTGATTATGGATTTAAATTAACACCAAATAAAG
AAAATAAAAATAATATTAGAGTTGAAAATGATAAATATAGTATTGAAATATATGCACCAG
AGAAACAGTTAAAAGTTTCAGGTGGAAAGAAAAGAATAACATCAATGGGTGTTAGTCATT
TAGGAGAGTTGGGTGTATATGGTAGTACTGATGGTACATTGGAAGTATTTGAAACTGGTG
ATGGTCAAATTAGAAGAAAATTAGATGGTCATGTTGGTGATGTTGATTTGGCAATGTTTT
TCCCAAGTGGTAGGGTTATACTAAGTGGTTCCTCTGATAGTAGATTAAAGATTTGGGATG
CTATAGAAGGCACATGCGNNNNNNNNNN