GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asnB in Shewanella loihica PV-4

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 5209024 Shew_1509 asparagine synthetase B (RefSeq)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__PV4:5209024
          Length = 552

 Score =  800 bits (2066), Expect = 0.0
 Identities = 388/554 (70%), Positives = 459/554 (82%), Gaps = 3/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIF + DI+TDA  LR+ ALE+S+L+RHRGPDWSGIYASD AILAHERL+IVD+  GA
Sbjct: 1   MCSIFAILDIQTDATPLRQVALEMSKLLRHRGPDWSGIYASDKAILAHERLAIVDIEHGA 60

Query: 61  QPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQG 120
           QPL ++ ++ +LAVNGEIYNH+ L+AE GD+Y +QT SDCEVILALYQE G EFLD L G
Sbjct: 61  QPLLSEDESLILAVNGEIYNHKELKAELGDKYSYQTNSDCEVILALYQEYGTEFLDKLNG 120

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD   D+YLIGRDH+GIIPLY G+D  G  YVASEMKAL+PVC+T++ F  G Y
Sbjct: 121 IFAFVLYDKRSDSYLIGRDHMGIIPLYTGHDAEGNFYVASEMKALMPVCKTVETFKPGHY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           L ++ GE   YY RDW  ++AV+DN     ELR+ALE +VK  LMSDVPYGVLLSGGLDS
Sbjct: 181 L-TKSGETH-YYQRDWQSFEAVQDNAASVEELREALEAAVKRQLMSDVPYGVLLSGGLDS 238

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S++SAIT+ +A RR+ED   S+AWWPQLHSFAVGL G+PDL AAQ+VA+ +GT+HHEI F
Sbjct: 239 SVVSAITQTFAKRRIEDDGASDAWWPQLHSFAVGLTGAPDLAAAQKVADAIGTIHHEITF 298

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           + QEGLDA++DVIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY
Sbjct: 299 SFQEGLDALKDVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 358

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNA+  HEE VRKL  LH++DC RANKAM+AWG+EARVPFLDK F+D AMRINP+ 
Sbjct: 359 FHKAPNAQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKAFIDTAMRINPEA 418

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KM  +G++EKHILR+ FE  LP  VAWRQKEQFSDGVGYSWID LKE AA QV D QL  
Sbjct: 419 KMSKDGRIEKHILRQAFEHKLPQEVAWRQKEQFSDGVGYSWIDGLKEHAAAQVDDLQLAN 478

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A+FRFPYNTP +KEAY YR  FEE FPLPSAAE VPGG SVACS+ +A+ WDE+ + + D
Sbjct: 479 AKFRFPYNTPETKEAYFYRCFFEEHFPLPSAAETVPGGKSVACSTPEALAWDESLQGIID 538

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV  VH+SAY
Sbjct: 539 PSGRAVQSVHESAY 552


Lambda     K      H
   0.319    0.135    0.407 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 927
Number of extensions: 27
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 554
Length of database: 552
Length adjustment: 36
Effective length of query: 518
Effective length of database: 516
Effective search space:   267288
Effective search space used:   267288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate 5209024 Shew_1509 (asparagine synthetase B (RefSeq))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.10304.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10304.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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