Alignments for a candidate for asnB in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asnB in Shewanella oneidensis MR-1

Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate 201902 SO2767 asparagine synthetase B, glutamine-hydrolyzing (NCBI ptt file)

Query= CharProtDB::CH_002444
         (554 letters)



>FitnessBrowser__MR1:201902
          Length = 554

 Score =  809 bits (2089), Expect = 0.0
 Identities = 392/554 (70%), Positives = 461/554 (83%), Gaps = 1/554 (0%)

Query: 1   MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60
           MCSIF + DI++DA ELR+ ALE+S+LMRHRGPDWSGIYASD AILAHERL+IVD+  GA
Sbjct: 1   MCSIFSILDIQSDAKELRQVALEMSKLMRHRGPDWSGIYASDKAILAHERLAIVDIEHGA 60

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

Query: 121 MFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSY 180
           +FAF LYD  KDAYLIGRDH+GIIPLY G D  G LYVASEMKAL+PVC+T++EF  G Y
Sbjct: 121 IFAFVLYDKAKDAYLIGRDHMGIIPLYTGRDAAGNLYVASEMKALMPVCKTVEEFQPGQY 180

Query: 181 LWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDS 240
           L+S D     YY RDW  YDAVKDN   + ELR+ALE +VK  LMSDVPYGVLLSGGLDS
Sbjct: 181 LYSSDAAAVKYYTRDWQQYDAVKDNGASQEELREALEAAVKRQLMSDVPYGVLLSGGLDS 240

Query: 241 SIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHF 300
           S+ISAIT+ +A RR+ED   + AWWPQLHSFAVGL G+PDL AA++VA+ +GT+HHEI+F
Sbjct: 241 SVISAITQTFAKRRIEDDGETGAWWPQLHSFAVGLKGAPDLIAAKKVADAIGTIHHEINF 300

Query: 301 TVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLY 360
           T QEGLDAI++VIYH+ETYDVTTIRA+TPMYLM+RKIKAMGIKMVLSGEG+DE+FGGYLY
Sbjct: 301 TFQEGLDAIKEVIYHLETYDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLY 360

Query: 361 FHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQD 420
           FHKAPNA+  HEE VRKL  LH++DC RANKAM+AWG+EARVPFLDK+F+DVAMRINP+ 
Sbjct: 361 FHKAPNAQAFHEELVRKLDKLHLFDCLRANKAMAAWGLEARVPFLDKEFMDVAMRINPEA 420

Query: 421 KMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLET 480
           KM  +G++EKHILR+ FE  LP  VAWRQKEQFSDGVGYSWID LK  AA+QV D QL  
Sbjct: 421 KMSKDGRIEKHILRQAFEHKLPKEVAWRQKEQFSDGVGYSWIDGLKAHAAEQVDDLQLAN 480

Query: 481 ARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDD 540
           A+FRFPYNTP +KEAY YR  FEE +PLPSAAE VPGG SVACS+ +A+ WDE+ + + D
Sbjct: 481 AKFRFPYNTPETKEAYFYRCFFEEHYPLPSAAETVPGGKSVACSTPEALAWDESLRGIID 540

Query: 541 PSGRAV-GVHQSAY 553
           PSGRAV  VH ++Y
Sbjct: 541 PSGRAVRSVHAASY 554


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: 924
Number of extensions: 27
Number of successful extensions: 1
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: 554
Length adjustment: 36
Effective length of query: 518
Effective length of database: 518
Effective search space:   268324
Effective search space used:   268324
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 201902 SO2767 (asparagine synthetase B, glutamine-hydrolyzing (NCBI ptt file))
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.758.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   6.3e-148  479.9   2.6   7.1e-124  400.5   0.2    2.4  2  lcl|FitnessBrowser__MR1:201902  SO2767 asparagine synthetase B, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201902  SO2767 asparagine synthetase B, glutamine-hydrolyzing (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.5   0.2  7.1e-124  7.1e-124       1     385 [.       2     372 ..       2     381 .. 0.96
   2 !   80.2   0.5   8.4e-27   8.4e-27     437     517 .]     372     453 ..     371     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: 400.5 bits;  conditional E-value: 7.1e-124
                       TIGR01536   1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek.evvivfnGE 78 
                                     C+i++i+d + +ake ++ + em+++++hRGPD++g++ +   ++ail+h+RLai+d+++gaQPl  e+ + ++ +nGE
  lcl|FitnessBrowser__MR1:201902   2 CSIFSILDIQSDAKELRQVALEMSKLMRHRGPDWSGIYAS---DKAILAHERLAIVDIEHGAQPLLTEDgSLILAVNGE 77 
                                     ***************889********************99...79************************999******* PP

                       TIGR01536  79 IYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelflaRDrlGikPLYyase.qgk 156
                                     IYNh+eL+++l +k y+++t+sD+EViLa+y+e+g e++++L+G FAf+l+d++k+++++ RD++Gi PLY +++ +g+
  lcl|FitnessBrowser__MR1:201902  78 IYNHKELKAQLGDK-YSYQTNSDCEVILALYQEYGTEFLDKLNGIFAFVLYDKAKDAYLIGRDHMGIIPLYTGRDaAGN 155
                                     **************.************************************************************9*** PP

                       TIGR01536 157 llfaSEiKallalk.eikaeldkealaelltlqlvptektlfkevkelepakaldgeekleeywevekeevkeseeelv 234
                                     l++aSE+Kal++++ +++++ ++++l +  +  +    k++ +++++++++k++ g ++ e                  
  lcl|FitnessBrowser__MR1:201902 156 LYVASEMKALMPVCkTVEEFQPGQYLYSSDAAAV----KYYTRDWQQYDAVKDN-G-ASQE------------------ 210
                                     **************9999999*****99999996....8*************97.4.3333.................. PP

                       TIGR01536 235 eelrelledavkkrlvadvpvgvllSGGlDSslvaaiakkeak.............sevktFsigfedskdldeskaar 300
                                      elre+le+avk++l++dvp+gvllSGGlDSs+++ai++ +ak              ++++F++g+++ +dl    aa+
  lcl|FitnessBrowser__MR1:201902 211 -ELREALEAAVKRQLMSDVPYGVLLSGGLDSSVISAITQTFAKrrieddgetgawwPQLHSFAVGLKGAPDLI---AAK 285
                                     .5******************************************************9****************...*** PP

                       TIGR01536 301 kvadelgtehkevliseeevlkeleevilale..eptairasiplyllsklarekgvkVvLsGeGaDElfgGYeyfrea 377
                                     kvad++gt h+e+ ++ +e+l++++evi++le  ++t+ira++p+yl++++++++g+k+vLsGeGaDElfgGY yf++a
  lcl|FitnessBrowser__MR1:201902 286 KVADAIGTIHHEINFTFQEGLDAIKEVIYHLEtyDVTTIRAATPMYLMARKIKAMGIKMVLSGEGADELFGGYLYFHKA 364
                                     ******************************************************************************* PP

                       TIGR01536 378 kaeealel 385
                                     ++++a++ 
  lcl|FitnessBrowser__MR1:201902 365 PNAQAFHE 372
                                     *****983 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 8.4e-27
                       TIGR01536 437 eellrldlelllsdllrakDrvsmahslEvRvPflDkelvelalsippelklr..dgkeKvlLreaaeellPeeileRk 513
                                     eel+r+  +l+l d+lra+ ++++a++lE+RvPflDke++++a++i+pe+k++     eK++Lr+a+e+ lP+e+++R+
  lcl|FitnessBrowser__MR1:201902 372 EELVRKLDKLHLFDCLRAN-KAMAAWGLEARVPFLDKEFMDVAMRINPEAKMSkdGRIEKHILRQAFEHKLPKEVAWRQ 449
                                     567778889999*******.********************************987789********************* PP

                       TIGR01536 514 Keaf 517
                                     Ke+f
  lcl|FitnessBrowser__MR1:201902 450 KEQF 453
                                     **99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (517 nodes)
Target sequences:                          1  (554 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: 00:00:00.08
# Mc/sec: 3.33
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis