Alignments for a candidate for gatB in Ruegeria conchae TW15

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Ruegeria conchae TW15

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_010442821.1 G7G_RS0117865 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000192475.1:WP_010442821.1
          Length = 485

 Score =  380 bits (976), Expect = e-110
 Identities = 201/466 (43%), Positives = 295/466 (63%), Gaps = 15/466 (3%)

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

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

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

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

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

Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349
             +PELPD++KA++++E  L  YDA VLT   E + +FE  +  G   KL +NW++  + 
Sbjct: 321 AKLPELPDDKKARFISEFSLTDYDASVLTAEVESAAYFEE-VAKGRSGKLAANWVINELF 379

Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409
             L K   ++ ++ ++P  LAG+I LI    +S KIAK +F  +  +GG+  QI+E+ G+
Sbjct: 380 GRLKKEDHDITESPVSPAQLAGIIDLISSDAISGKIAKDLFEIVYTEGGDPAQIVEERGM 439

Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKAS 455
            Q++D   +   ++E +  N   VE  K    K  G+ VGQ+MKA+
Sbjct: 440 KQVTDTGAIEAALDEIIAANPAQVEKAKVNP-KLAGWFVGQVMKAT 484


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: 611
Number of extensions: 28
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: 485
Length adjustment: 34
Effective length of query: 441
Effective length of database: 451
Effective search space:   198891
Effective search space used:   198891
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 WP_010442821.1 G7G_RS0117865 (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.1007827.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.8e-153  495.0   0.0   1.1e-152  494.8   0.0    1.0  1  NCBI__GCF_000192475.1:WP_010442821.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010442821.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.8   0.0  1.1e-152  1.1e-152       3     463 ..      20     484 ..      18     485 .] 0.95

  Alignments for each domain:
  == domain 1  score: 494.8 bits;  conditional E-value: 1.1e-152
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++elviG+EvH q+  ++KlF+ +s+++   +pN+nv  v+ ++PG lPv+N+  v++A+  +l l++ i+  
  NCBI__GCF_000192475.1:WP_010442821.1  20 DWELVIGMEVHAQVSSNAKLFSGASTQFGA-EPNSNVAFVDAAMPGMLPVINEYCVEQAVRTGLGLKADIN-L 90 
                                           789*************************99.**************************************77.5 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147
                                           +s FdRK+YfYpDlP+gyqi+q ++Pi+ +G++ +e+ ++  + ++ier+h+E+D+gks +  +  +++s+vD
  NCBI__GCF_000192475.1:WP_010442821.1  91 KSAFDRKNYFYPDLPQGYQISQLYQPIVGEGEVLVEMGDGTaRMVRIERIHMEQDAGKSIHDMD--PHMSFVD 161
                                           9***********************************97655499*****************976..78***** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........e 210
                                           +NR+gv L+EiV++Pd++ ++ea+a++ klrqi+ryl+  dg++++G++R+DvNvsi l G           +
  NCBI__GCF_000192475.1:WP_010442821.1 162 LNRTGVCLMEIVSRPDIRGPEEAAAYIAKLRQIMRYLGTCDGNMQNGNLRADVNVSICLPGAyekyqetqdfS 234
                                           *********************************************************9876421111111223 PP

                             TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlp 283
                                           + gtr EiKN+ns++ i++aie E  Rq+++++ g ++ qetr +d  k  t s+R+Kee++DYRYfp+Pdl 
  NCBI__GCF_000192475.1:WP_010442821.1 235 HLGTRCEIKNMNSMRFIQQAIEVEARRQIAIVEGGGTIDQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLL 307
                                           5689********************************************************************* PP

                             TIGR00133 284 pieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileel 356
                                           p+ei++ +v++ +++klpelP+ k++r+ +e+ l ++da vl++++e + +feev+k  +  kla+nW+++el
  NCBI__GCF_000192475.1:WP_010442821.1 308 PLEIEQAWVDD-IAAKLPELPDDKKARFISEFSLTDYDASVLTAEVESAAYFEEVAKGRSG-KLAANWVINEL 378
                                           **********9.********************************************98877.*********** PP

                             TIGR00133 357 lgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvki 429
                                            g+L+k++ +++e+ ++p +la +i+li+ + is+k+ak+l+e + ++++dp +++e++g+ q++d+ ++ ++
  NCBI__GCF_000192475.1:WP_010442821.1 379 FGRLKKEDHDITESPVSPAQLAGIIDLISSDAISGKIAKDLFEIVYTEGGDPAQIVEERGMKQVTDTGAIEAA 451
                                           ************************************************************************* PP

                             TIGR00133 430 veevikenpkevekyksgkekalkflvGqvmkkt 463
                                           ++e+i+ np +vek k +  k+ +++vGqvmk t
  NCBI__GCF_000192475.1:WP_010442821.1 452 LDEIIAANPAQVEKAKVN-PKLAGWFVGQVMKAT 484
                                           *************98755.57889********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (485 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: 17.24
//
[ok]

This GapMind analysis is from Jul 26 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 2024 update 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 original 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