Alignments for a candidate for gatB in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Mycolicibacterium vanbaalenii PYR-1

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_011779346.1 MVAN_RS10615 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000015305.1:WP_011779346.1
          Length = 503

 Score =  378 bits (970), Expect = e-109
 Identities = 209/482 (43%), Positives = 301/482 (62%), Gaps = 17/482 (3%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E V+GLEVHVEL T +K+F      FGAE NTQ   + LG PG LPVLN+ AVE A++ 
Sbjct: 21  YEPVLGLEVHVELSTATKMFCGCANRFGAEPNTQVCPVCLGLPGSLPVLNQSAVEAAIRI 80

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGITRL 121
            +ALNC+IA   +F RKNYFYPD PK YQISQ+D+PI  NG +++ +  G T R+ I R 
Sbjct: 81  GLALNCDIAPWGRFARKNYFYPDQPKNYQISQYDEPIAINGHLDVPLDDGTTWRVDIERA 140

Query: 122 HLEEDAGKLTHTGDG--------YSLVDFNRQGTPLVEIVSEP----DIRTPEEAYAYLE 169
           H+EED GKLTH G           SL D+NR G PL+EIV++P      R PE A AY+ 
Sbjct: 141 HMEEDTGKLTHLGSDTGRIAGATTSLADYNRSGVPLIEIVTKPIEGTGERAPEIARAYVT 200

Query: 170 KLKSIIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEE 229
            L+ +++   VSD +M++GS+RCD+N+SL+PIGQ EFGT+TE KN+NS   V+  + +E 
Sbjct: 201 ALRDLLRALDVSDVRMDQGSMRCDSNVSLKPIGQAEFGTRTETKNVNSLKSVEVAVRYEM 260

Query: 230 KRQEQVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERV 289
           +RQ  +L SG  + QETR + E    T   R KE + DYRYFPEPDL  +    E  E++
Sbjct: 261 RRQAAILESGATVHQETRHFHE-DGHTSPGRSKETAQDYRYFPEPDLEPVAPSAELVEQL 319

Query: 290 KASIPELPDERRKRYIEELGFAAYDAMVLTLTKEMA-DFFEETVQKGAEAKQASNWLMGE 348
           + +IPELP   RKR  ++ G +  D ++  L    A D    TV+ GA + QA  W    
Sbjct: 320 RTTIPELPWLARKRIQQDWGIS--DEVMRDLVNIGALDLIAATVEHGASSDQARAWWGNF 377

Query: 349 VSAYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEK 408
           +    N    EL  + +TP  +A ++KL+E G +S+K+A++V + ++   GD E+++ ++
Sbjct: 378 LVQKANESGVELEALPITPAQVAAVVKLVEDGKLSNKLARQVVEGVLAGEGDPEQVMADR 437

Query: 409 GLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKI 468
           GL  + D+ ++   V EAL  NP  +E  + GK +A G +VG +MKA+KGQA+   V ++
Sbjct: 438 GLAVVRDDSLIQAAVDEALAANPDVVEKIRGGKVQAAGAIVGAVMKATKGQADAARVREL 497

Query: 469 LL 470
           ++
Sbjct: 498 VM 499


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: 553
Number of extensions: 27
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: 503
Length adjustment: 34
Effective length of query: 442
Effective length of database: 469
Effective search space:   207298
Effective search space used:   207298
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 WP_011779346.1 MVAN_RS10615 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
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.30782.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-147  477.4   0.0   2.7e-147  477.1   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779346.1  MVAN_RS10615 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779346.1  MVAN_RS10615 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.1   0.0  2.7e-147  2.7e-147       3     476 ..      20     498 ..      18     502 .. 0.95

  Alignments for each domain:
  == domain 1  score: 477.1 bits;  conditional E-value: 2.7e-147
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               +ye v+GlEvHv l t++K+Fc c n++   +pNt+vcpvclglPG+lPvlN++av++A+ ++laln+ 
  lcl|NCBI__GCF_000015305.1:WP_011779346.1  20 KYEPVLGLEVHVELSTATKMFCGCANRFGA-EPNTQVCPVCLGLPGSLPVLNQSAVEAAIRIGLALNCD 87 
                                               7999************************99.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139
                                                +++   F+RK+YfYpD+Pk+yqi+q+d Pia +G+l++ l+++   ++ ier h+EeDtgk+++ +sd
  lcl|NCBI__GCF_000015305.1:WP_011779346.1  88 -IAPWGRFARKNYFYPDQPKNYQISQYDEPIAINGHLDVPLDDGTtWRVDIERAHMEEDTGKLTHLGSD 155
                                               .668***********************************999876589********************9 PP

                                 TIGR00133 140 k.....dkqslvDfNRsgvPLlEiVtkPdl....ksakearaflkklrqilryleisdgdleeGsmRvD 199
                                               +     ++ sl D+NRsgvPL+EiVtkP      + ++ ara++  lr +lr l++sd  +++GsmR+D
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 156 TgriagATTSLADYNRSGVPLIEIVTKPIEgtgeRAPEIARAYVTALRDLLRALDVSDVRMDQGSMRCD 224
                                               988888899*******************8711224456689**************************** PP

                                 TIGR00133 200 vNvsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkK 268
                                                Nvs+++ Gq ++gtr E KN+nslks+e a+ yE+ Rq ++l++g +v+qetr+f+e    t   R+K
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 225 SNVSLKPIGQAEFGTRTETKNVNSLKSVEVAVRYEMRRQAAILESGATVHQETRHFHEDG-HTSPGRSK 292
                                               ********************************************************9875.68899*** PP

                                 TIGR00133 269 eeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafee 337
                                               e+++DYRYfpePdl p+  + e+v++ +++++pelP  +r+r++++ g+s+e  + lv+    ld    
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 293 ETAQDYRYFPEPDLEPVAPSAELVEQ-LRTTIPELPWLARKRIQQDWGISDEVMRDLVN-IGALDLIAA 359
                                               ************************99.*****************************996.566677777 PP

                                 TIGR00133 338 vvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkk 406
                                                v+  +++++a  W  + l+++ n++ ++l++  ++p ++a+++kl+++gk+s+k a++++e +l  ++
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 360 TVEHGASSDQARAWWGNFLVQKANESGVELEALPITPAQVAAVVKLVEDGKLSNKLARQVVEGVLAGEG 428
                                               777777889999********************************************************* PP

                                 TIGR00133 407 dpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekl 475
                                               dp++++  +gl  ++d++ ++++v+e+++ np+ vek + gk +a + +vG vmk tkg+ad+++v +l
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 429 DPEQVMADRGLAVVRDDSLIQAAVDEALAANPDVVEKIRGGKVQAAGAIVGAVMKATKGQADAARVREL 497
                                               ******************************************************************999 PP

                                 TIGR00133 476 l 476
                                               +
  lcl|NCBI__GCF_000015305.1:WP_011779346.1 498 V 498
                                               7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (503 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: 00:00:00.02
# Mc/sec: 10.97
//
[ok]

This GapMind analysis is from Apr 10 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