Alignments for a candidate for gatB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Phaeobacter inhibens BS107

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate GFF968 PGA1_c09840 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Phaeo:GFF968
          Length = 504

 Score =  397 bits (1021), Expect = e-115
 Identities = 211/484 (43%), Positives = 310/484 (64%), Gaps = 16/484 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIG+EVH ++ +++K+FS +   FGAEPNSN   +D A PG+LPV+N   V+ A+R 
Sbjct: 21  WELVIGMEVHAQVSSNAKLFSGASTKFGAEPNSNVAFVDAAMPGMLPVINDYCVEQAVRT 80

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            + L  +I   S FDRKNYFYPD P+ YQISQ   PI   G + +E+ DG  + + + R+
Sbjct: 81  GLGLKADINLWSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTARNVRVERI 140

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           HME+DAGKS H  +   S VDLNR G  L+EIVS PDIR P+EA AY+ KLR I+QY G 
Sbjct: 141 HMEQDAGKSIHDMDPNMSFVDLNRTGVCLMEIVSRPDIRGPEEAAAYIAKLRQIMQYLGT 200

Query: 180 SDVKMEEGSLRCDANISL-RPYGQEKF---------GTKAELKNLNSFNYVRKGLEYEEK 229
            D  M+ G+LR D N+S+ RP   EK+         GT+ E+KN+NS  ++++ ++ E +
Sbjct: 201 CDGNMQNGNLRADVNVSVCRPGQYEKYQETQDFSHLGTRCEIKNMNSMRFIQQAIDVEAR 260

Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289
           RQ   + +GG I QETR +D   G+T  MR KE + DYRYFP+PD++PL I+ AW + + 
Sbjct: 261 RQIAIIEAGGTIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQAWVDDIA 320

Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349
             +PELPDE+KA+++ + GL  YDA VLT   E + FFE T + G   KL +NW++  + 
Sbjct: 321 ANLPELPDEKKARFIKDFGLSDYDASVLTADVESATFFEQTAK-GRSGKLAANWVINELF 379

Query: 350 EYLNKNQ-VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNG 408
             L K++  ++ D+ ++P  L G+I LI    +S KIAK +F  +  +GG+  QI+E+ G
Sbjct: 380 GRLKKDEDKQITDSPVSPAQLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAQIVEERG 439

Query: 409 LVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLL 468
           + Q++D   +   ++E +  N   VE  K    K  G+ VGQ+MKA+ G+ANP+ VN+L+
Sbjct: 440 MKQVTDTGAIEAALDEIIAANPAQVEKAKVNP-KLAGWFVGQVMKATGGKANPKAVNELV 498

Query: 469 KQEL 472
            ++L
Sbjct: 499 AKKL 502


Lambda     K      H
   0.313    0.133    0.373 

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: 654
Number of extensions: 31
Number of successful extensions: 6
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: 475
Length of database: 504
Length adjustment: 34
Effective length of query: 441
Effective length of database: 470
Effective search space:   207270
Effective search space used:   207270
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate GFF968 PGA1_c09840 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

# 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.28736.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-156  507.2   0.0   2.4e-156  506.9   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF968  PGA1_c09840 aspartyl/glutamyl-tR


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF968  PGA1_c09840 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.9   0.0  2.4e-156  2.4e-156       3     480 ..      20     502 ..      18     503 .. 0.95

  Alignments for each domain:
  == domain 1  score: 506.9 bits;  conditional E-value: 2.4e-156
                         TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvF 79 
                                       ++elviG+EvH q+  ++KlF+ +s+++   +pN+nv  v+ ++PG lPv+N   v++A+  +l l++ i+   s F
  lcl|FitnessBrowser__Phaeo:GFF968  20 DWELVIGMEVHAQVSSNAKLFSGASTKFGA-EPNSNVAFVDAAMPGMLPVINDYCVEQAVRTGLGLKADIN-LWSAF 94 
                                       789*************************99.**************************************76.5**** PP

                         TIGR00133  80 dRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPL 155
                                       dRK+YfYpDlP+gyqi+q + Pi+ +G++ +el ++  +++++er+h+E+D+gks +  +  +++s+vD+NR+gv L
  lcl|FitnessBrowser__Phaeo:GFF968  95 DRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTaRNVRVERIHMEQDAGKSIHDMD--PNMSFVDLNRTGVCL 169
                                       ********************************9765449******************966..79************* PP

                         TIGR00133 156 lEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........ekegtrvEiKNln 222
                                       +EiV++Pd++ ++ea+a++ klrqi++yl+  dg++++G++R+DvNvs+   Gq          ++ gtr EiKN+n
  lcl|FitnessBrowser__Phaeo:GFF968 170 MEIVSRPDIRGPEEAAAYIAKLRQIMQYLGTCDGNMQNGNLRADVNVSVCRPGQyekyqetqdfSHLGTRCEIKNMN 246
                                       *************************************************98877222222222235679******** PP

                         TIGR00133 223 slksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveek 299
                                       s++ i++ai+ E  Rq+++++ g ++ qetr +d  k  t s+R+Kee++DYRYfp+Pdl p+ei++ +v++ ++++
  lcl|FitnessBrowser__Phaeo:GFF968 247 SMRFIQQAIDVEARRQIAIIEAGGTIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQAWVDD-IAAN 322
                                       ***********************************************************************9.**** PP

                         TIGR00133 300 lpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnk.kkislaeallkpe 375
                                       lpelP++k++r+ k++gls++da vl++d+e +  fe+ +k  +  kla+nW+++el g+L+k ++ +++++ ++p 
  lcl|FitnessBrowser__Phaeo:GFF968 323 LPELPDEKKARFIKDFGLSDYDASVLTADVESATFFEQTAKGRSG-KLAANWVINELFGRLKKdEDKQITDSPVSPA 398
                                       **************************************9998777.***************8735799********* PP

                         TIGR00133 376 elaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekal 452
                                       +l  +i+li+ + is+k+ak+l+e + ++++dp +++e++g+ q++d+ ++ ++++e+i+ np +vek k +  k+ 
  lcl|FitnessBrowser__Phaeo:GFF968 399 QLGGIIDLISSDAISGKIAKDLFEIVYTEGGDPAQIVEERGMKQVTDTGAIEAALDEIIAANPAQVEKAKVN-PKLA 474
                                       *******************************************************************98755.5788 PP

                         TIGR00133 453 kflvGqvmkktkgradpkevekllkell 480
                                       +++vGqvmk t g+a+pk v++l+ ++l
  lcl|FitnessBrowser__Phaeo:GFF968 475 GWFVGQVMKATGGKANPKAVNELVAKKL 502
                                       9***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (504 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.35
//
[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