Alignments for a candidate for gatB in Phaeacidiphilus oryzae TH49

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Phaeacidiphilus oryzae TH49

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_037572601.1 BS73_RS14765 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000744815.1:WP_037572601.1
          Length = 500

 Score =  400 bits (1029), Expect = e-116
 Identities = 212/484 (43%), Positives = 309/484 (63%), Gaps = 14/484 (2%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           ++ V+GLEVHVEL T++K+F    T  GA  N+Q     LG PG LPV+N   VE A+K 
Sbjct: 16  YDPVMGLEVHVELGTRTKMFCGCSTELGAAPNSQVCPTCLGLPGALPVVNATGVESAIKI 75

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGITRL 121
            +ALNCEIA   +F RKNYFYPD PK +Q SQ+D+PI  NG++++++  G+  R+ I R 
Sbjct: 76  GLALNCEIAEWCRFARKNYFYPDMPKNFQTSQYDEPIAFNGYLDVQLEDGEVFRVEIERA 135

Query: 122 HLEEDAGKLTHTGDG--------YSLVDFNRQGTPLVEIVSEP----DIRTPEEAYAYLE 169
           H+EED GK TH G          +SL+D+NR G PL+EIV++P      R PE A AY+ 
Sbjct: 136 HMEEDTGKSTHVGGATGRIHGASHSLLDYNRAGIPLIEIVTKPIEGAGRRAPEVARAYVA 195

Query: 170 KLKSIIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEE 229
           +L+ +I+  GVS+ +ME+G +RCD N+SLRPIG+E+FGT++E KN+NS   V++ + +E 
Sbjct: 196 ELRELIRALGVSEARMEQGQMRCDVNLSLRPIGREKFGTRSETKNVNSLRSVERAVRYEI 255

Query: 230 KRQEQVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERV 289
           +R   VL  G  I QETR + E    T   RVKE ++DYRYFPEPDLV +    EW E +
Sbjct: 256 ERHAAVLDEGGTIVQETRHFHEDDGTTTSGRVKEEAEDYRYFPEPDLVPVAPSREWVEEL 315

Query: 290 KASIPELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEV 349
           +A +PELP  RR R   E G +  D M   +     D  E T+ +GA A QA  W +GE+
Sbjct: 316 RAGLPELPRVRRARLQAEWGLSDKD-MQAAVNAGAVDLIEATIAEGAPADQARKWWLGEL 374

Query: 350 SAYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKG 409
           S   N  Q+ELA + +TP  +A +  L+++G ++ K+A++V   +++  G+ +++V+++G
Sbjct: 375 SRTANETQRELAALPITPAQVARVSALVKEGKLNDKLARQVIDGVLKGEGEPDEVVEKRG 434

Query: 410 LVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           L  +SDEG L   V EA+  NP   E  + GK  A G LVG +MKA++GQA+   V +++
Sbjct: 435 LAVVSDEGALTTAVEEAIAANPGVAEKIRGGKVAAAGALVGAVMKATRGQADAARVKELI 494

Query: 470 LEEI 473
           LE++
Sbjct: 495 LEKL 498


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: 588
Number of extensions: 31
Number of successful extensions: 5
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: 500
Length adjustment: 34
Effective length of query: 442
Effective length of database: 466
Effective search space:   205972
Effective search space used:   205972
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_037572601.1 BS73_RS14765 (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.3685763.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-151  489.7   0.0   4.6e-151  489.5   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037572601.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572601.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.5   0.0  4.6e-151  4.6e-151       3     480 ..      15     498 ..      13     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 489.5 bits;  conditional E-value: 4.6e-151
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                            y+ v+GlEvHv l+t++K+Fc cs+e+    pN++vcp clglPGalPv+N   v++A+k++laln++ ++e
  NCBI__GCF_000744815.1:WP_037572601.1  15 TYDPVMGLEVHVELGTRTKMFCGCSTELGA-APNSQVCPTCLGLPGALPVVNATGVESAIKIGLALNCE-IAE 85 
                                           58889***********************99.9*************************************.668 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdk.....dk 142
                                              F+RK+YfYpD+Pk++q +q+d Pia +G+l+++le++e  +++ier h+EeDtgks++ +  +     ++
  NCBI__GCF_000744815.1:WP_037572601.1  86 WCRFARKNYFYPDMPKNFQTSQYDEPIAFNGYLDVQLEDGEvFRVEIERAHMEEDTGKSTHVGGATgrihgAS 158
                                           **************************************999789*****************987766677899 PP

                             TIGR00133 143 qslvDfNRsgvPLlEiVtkPd....lksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqek 211
                                           +sl+D+NR+g+PL+EiVtkP      + ++ ara++ +lr+++r l++s++ +e+G mR+DvN+s+r+ G+ek
  NCBI__GCF_000744815.1:WP_037572601.1 159 HSLLDYNRAGIPLIEIVTKPIegagRRAPEVARAYVAELRELIRALGVSEARMEQGQMRCDVNLSLRPIGREK 231
                                           ********************733334778899***************************************** PP

                             TIGR00133 212 egtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlpp 284
                                           +gtr E KN+nsl+s+e+a+ yEieR  ++l +g +++qetr+f+e   +t s R Kee+eDYRYfpePdl+p
  NCBI__GCF_000744815.1:WP_037572601.1 232 FGTRSETKNVNSLRSVERAVRYEIERHAAVLDEGGTIVQETRHFHEDDGTTTSGRVKEEAEDYRYFPEPDLVP 304
                                           ************************************************************************* PP

                             TIGR00133 285 ieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileell 357
                                           +  + e+v+e +++ lpelP+ +r+rl+ e gls++d +  v+ +  +d  e      +++++a +W l el 
  NCBI__GCF_000744815.1:WP_037572601.1 305 VAPSREWVEE-LRAGLPELPRVRRARLQAEWGLSDKDMQAAVN-AGAVDLIEATIAEGAPADQARKWWLGELS 375
                                           **********.****************************9885.66789999999999999************ PP

                             TIGR00133 358 geLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiv 430
                                           ++ n+++ +la+  ++p ++a++ +l+kegk+++k a+++++ +l+ +++p++++ek+gl  +sde +l+ +v
  NCBI__GCF_000744815.1:WP_037572601.1 376 RTANETQRELAALPITPAQVARVSALVKEGKLNDKLARQVIDGVLKGEGEPDEVVEKRGLAVVSDEGALTTAV 448
                                           ************************************************************************* PP

                             TIGR00133 431 eevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           ee+i+ np+  ek + gk +a + lvG vmk t+g+ad+++v++l+ e+l
  NCBI__GCF_000744815.1:WP_037572601.1 449 EEAIAANPGVAEKIRGGKVAAAGALVGAVMKATRGQADAARVKELILEKL 498
                                           **********************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (500 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: 00:00:00.00
# Mc/sec: 30.80
//
[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