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))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01536.hmm
# target sequence database:        /tmp/gapView.20352.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01536  [M=517]
Accession:   TIGR01536
Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.5e-148  481.2   1.6   1.2e-123  399.8   0.2    2.9  2  lcl|FitnessBrowser__PV4:5209024  Shew_1509 asparagine synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209024  Shew_1509 asparagine synthetase B (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.8   0.2  1.2e-123  1.2e-123       1     385 [.       2     370 ..       2     379 .. 0.96
   2 !   78.9   0.2   2.1e-26   2.1e-26     437     517 .]     370     451 ..     369     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: 399.8 bits;  conditional E-value: 1.2e-123
                        TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivfnG 77 
                                      C+i++i+d +++a+  ++ + em+++l+hRGPD++g++ +   ++ail+h+RLai+d+++gaQPl +e+ + ++ +nG
  lcl|FitnessBrowser__PV4:5209024   2 CSIFAILDIQTDATPLRQVALEMSKLLRHRGPDWSGIYAS---DKAILAHERLAIVDIEHGAQPLLSEDeSLILAVNG 76 
                                      ************999889********************99...79************************99999**** PP

                        TIGR01536  78 EIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase.q 154
                                      EIYNh+eL++el +k y+++t+sD+EViLa+y+e+g e++++L+G FAf+l+d++++ +++ RD++Gi PLY + + +
  lcl|FitnessBrowser__PV4:5209024  77 EIYNHKELKAELGDK-YSYQTNSDCEVILALYQEYGTEFLDKLNGIFAFVLYDKRSDSYLIGRDHMGIIPLYTGHDaE 153
                                      ***************.************************************************************99 PP

                        TIGR01536 155 gkllfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekeevkesee 231
                                      g++++aSE+Kal++++ +++++ ++++l++    +      +++++++ +e+++++  +++                 
  lcl|FitnessBrowser__PV4:5209024 154 GNFYVASEMKALMPVCkTVETFKPGHYLTKSGETH------YYQRDWQSFEAVQDN--AAS----------------- 206
                                      ****************8888888888888776666......79*********9997..333................. PP

                        TIGR01536 232 elveelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfedskdldes 296
                                        veelre+le+avk++l++dvp+gvllSGGlDSs+v+ai++ +ak              ++++F++g+++ +dl   
  lcl|FitnessBrowser__PV4:5209024 207 --VEELREALEAAVKRQLMSDVPYGVLLSGGLDSSVVSAITQTFAKrrieddgasdawwPQLHSFAVGLTGAPDLA-- 280
                                      ..567******************************************************9****************.. PP

                        TIGR01536 297 kaarkvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYe 372
                                       aa+kvad++gt h+e+++s +e+l++l++vi++le  ++t+ira++p+yl++++++++g+k+vLsGeGaDElfgGY 
  lcl|FitnessBrowser__PV4:5209024 281 -AAQKVADAIGTIHHEITFSFQEGLDALKDVIYHLEtyDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYL 357
                                      .***************************************************************************** PP

                        TIGR01536 373 yfreakaeealel 385
                                      yf++a++++a++ 
  lcl|FitnessBrowser__PV4:5209024 358 YFHKAPNAQAFHE 370
                                      **********983 PP

  == domain 2  score: 78.9 bits;  conditional E-value: 2.1e-26
                        TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeileR 512
                                      eel+r+  +l+l d+lra+ ++++a++lE+RvPflDk+++++a++i+pe+k++     eK++Lr+a+e+ lP+e+++R
  lcl|FitnessBrowser__PV4:5209024 370 EELVRKLDKLHLFDCLRAN-KAMAAWGLEARVPFLDKAFIDTAMRINPEAKMSkdGRIEKHILRQAFEHKLPQEVAWR 446
                                      567778889999*******.********************************987789******************** PP

                        TIGR01536 513 kKeaf 517
                                      +Ke+f
  lcl|FitnessBrowser__PV4:5209024 447 QKEQF 451
                                      ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (552 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.09u 0.02s 00:00:00.11 Elapsed: 00:00:00.09
# Mc/sec: 3.04
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory