GapMind for Amino acid biosynthesis

 

Aligments 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)



>lcl|FitnessBrowser__PV4:5209024 Shew_1509 asparagine synthetase B
           (RefSeq)
          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.11934.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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 3.68
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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