Alignments for a candidate for gatB in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Marinobacter adhaerens HP15

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate GFF2514 HP15_2458 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= metacyc::MONOMER-13956
         (476 letters)



>FitnessBrowser__Marino:GFF2514
          Length = 483

 Score =  421 bits (1081), Expect = e-122
 Identities = 221/481 (45%), Positives = 314/481 (65%), Gaps = 8/481 (1%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M ++ VIGLE+HV+L TK+KIFS S T +GAE NTQ + +DL  PG LPV N++A  +A+
Sbjct: 1   MQWDIVIGLEIHVQLATKTKIFSGSSTAYGAEPNTQANAVDLAMPGTLPVPNEQAFRYAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119
              +A+N EI   + F+RKNYFYPD PK YQ +Q ++PI   G+++I++  G+TKR+ I 
Sbjct: 61  MFGLAVNAEIERRSVFERKNYFYPDLPKGYQTTQLERPIVGPGFVDIDLPNGETKRVRIH 120

Query: 120 RLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYT 178
             HLEEDAGK  H    G + VD NR GTPL+E+V+EPD+   EEA A+ +KL SI+   
Sbjct: 121 HAHLEEDAGKSLHEDFHGMTGVDLNRAGTPLIEVVTEPDMNNAEEAVAFAKKLHSIVTSL 180

Query: 179 GVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLS 238
           G+ D  M +GS+R D NISL+P G +  GT+TE KNLNSF F+++ + HE +RQ  +L  
Sbjct: 181 GICDGDMSQGSMRFDVNISLKPKGSDTLGTRTETKNLNSFRFMEQAIAHEVERQMDILED 240

Query: 239 GFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298
           G  I QETR Y+    ++  MR KE ++DYRYFP PDL+ + IDD + E  + S+PELPD
Sbjct: 241 GGNIVQETRLYNGDRDESRSMRTKEEANDYRYFPCPDLLPVEIDDSFIEEARNSLPELPD 300

Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQK 358
            R+ R++E+ G   YDA +L+   ++A FFEE   +G +AK  +NW+ GE SA LNAE+K
Sbjct: 301 ARKARFMEQYGLNDYDAGLLSGDSKLATFFEEAASQGKDAKLVANWIQGEFSARLNAEEK 360

Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDA-EKIVKEKGLVQISDEG 417
            +AD  ++   L  ++  I   TISS  AKKVF+ L     D+ + I+  KGL Q+SD G
Sbjct: 361 SVADSPISGAQLGDLVVRIADNTISSAGAKKVFEALWSGENDSVDAIIDAKGLKQVSDTG 420

Query: 418 VLLKLVTEALDNNPQSIEDFKNGKD-----RAIGFLVGQIMKASKGQANPPMVNKILLEE 472
            L  +V E L   P  +  ++N +D     + +G  +G +MKASKGQ NP + N+IL+ +
Sbjct: 421 ALEAMVDEVLAGMPDQVAQYQNEEDPKKRKKMLGGFMGPLMKASKGQGNPKLFNEILVRK 480

Query: 473 I 473
           +
Sbjct: 481 L 481


Lambda     K      H
   0.314    0.134    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: 620
Number of extensions: 29
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: 476
Length of database: 483
Length adjustment: 34
Effective length of query: 442
Effective length of database: 449
Effective search space:   198458
Effective search space used:   198458
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: 51 (24.3 bits)

Align candidate GFF2514 HP15_2458 (aspartyl/glutamyl-tRNA 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.164487.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.2e-160  519.0   0.0   5.8e-160  518.8   0.0    1.0  1  FitnessBrowser__Marino:GFF2514  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Marino:GFF2514  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.8   0.0  5.8e-160  5.8e-160       3     480 ..       2     481 ..       1     482 [. 0.97

  Alignments for each domain:
  == domain 1  score: 518.8 bits;  conditional E-value: 5.8e-160
                       TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvFdR 81 
                                     ++++viGlE+Hvql tk+K+F+ +s+ +   +pNt+ ++v+l++PG+lPv+N++a + A++ +la+n++i +  svF+R
  FitnessBrowser__Marino:GFF2514   2 QWDIVIGLEIHVQLATKTKIFSGSSTAYGA-EPNTQANAVDLAMPGTLPVPNEQAFRYAVMFGLAVNAEI-ERRSVFER 78 
                                     7899************************99.**************************************5.569***** PP

                       TIGR00133  82 KhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEiV 159
                                     K+YfYpDlPkgyq tq ++Pi+  G ++i+l ++e k+++i++ hlEeD+gks ++    + ++ vD+NR+g+PL+E+V
  FitnessBrowser__Marino:GFF2514  79 KNYFYPDLPKGYQTTQLERPIVGPGFVDIDLPNGEtKRVRIHHAHLEEDAGKSLHEDF--HGMTGVDLNRAGTPLIEVV 155
                                     *******************************98777*******************944..589**************** PP

                       TIGR00133 160 tkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNlnslksiekaieyEieRq 238
                                     t+Pd+++a+ea+af kkl++i+  l+i dgd+ +GsmR DvN+s+++kG+++ gtr E KNlns++ +e+ai +E+eRq
  FitnessBrowser__Marino:GFF2514 156 TEPDMNNAEEAVAFAKKLHSIVTSLGICDGDMSQGSMRFDVNISLKPKGSDTLGTRTETKNLNSFRFMEQAIAHEVERQ 234
                                     ******************************************************************************* PP

                       TIGR00133 239 kkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeygl 317
                                     +++l++g +++qetr ++  +    s+R Kee++DYRYfp Pdl p+eid+++++e  ++ lpelP+a+++r++++ygl
  FitnessBrowser__Marino:GFF2514 235 MDILEDGGNIVQETRLYNGDRDESRSMRTKEEANDYRYFPCPDLLPVEIDDSFIEE-ARNSLPELPDARKARFMEQYGL 312
                                     ********************************************************.9********************* PP

                       TIGR00133 318 seedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksake 396
                                     +++da +l  d++l+  fee+++  k++kl++nWi  e+ ++Ln+++ s+a++ ++  +l  l+  i +++is+  ak+
  FitnessBrowser__Marino:GFF2514 313 NDYDAGLLSGDSKLATFFEEAASQGKDAKLVANWIQGEFSARLNAEEKSVADSPISGAQLGDLVVRIADNTISSAGAKK 391
                                     ******************************************************************************* PP

                       TIGR00133 397 lleellen.kkdpkklieklgliqisdekelvkiveevikenpkevekyk.....sgkekalkflvGqvmkktkgradp 469
                                     ++e l +  + +++++i+++gl q+sd+ +l ++v+ev++  p++v +y+     ++++k+l+ ++G  mk +kg+ +p
  FitnessBrowser__Marino:GFF2514 392 VFEALWSGeNDSVDAIIDAKGLKQVSDTGALEAMVDEVLAGMPDQVAQYQneedpKKRKKMLGGFMGPLMKASKGQGNP 470
                                     ****998647889************************************98888888999******************* PP

                       TIGR00133 470 kevekllkell 480
                                     k ++++l  +l
  FitnessBrowser__Marino:GFF2514 471 KLFNEILVRKL 481
                                     ******98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (483 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.52
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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