Alignments for a candidate for gatB in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Sulfurimonas denitrificans DSM 1251

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011372963.1 SUDEN_RS06970 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000012965.1:WP_011372963.1
          Length = 474

 Score =  390 bits (1001), Expect = e-113
 Identities = 210/479 (43%), Positives = 297/479 (62%), Gaps = 9/479 (1%)

Query: 70  YEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVRL 129
           +E VIG+E HVQL+T TK FCSC  ++    NT+ CP C+ LPGALPVLN +V+   +  
Sbjct: 2   FEVVIGLEVHVQLNTKTKLFCSCPTSFNHKQNTNTCPTCLALPGALPVLNKEVLNKSIMF 61

Query: 130 GLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRRFGI 189
           G A++  ++  S FDRK YFYPD P  YQI+Q   P+   G + +D      G H+   I
Sbjct: 62  GTAVDATINKTSYFDRKSYFYPDSPSAYQITQLYTPVVEHGKLRIDFE---DGSHKTIRI 118

Query: 190 TRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRIARY 249
            R H+E DAGK +H   G  S+VDLNRAG PLLEIVSEPDMRS  E   Y  ++  I RY
Sbjct: 119 NRAHIEADAGKNIHD--GAISKVDLNRAGTPLLEIVSEPDMRSAEEVTLYLKKLHSIIRY 176

Query: 250 LGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQALLYN 309
           L + + NMQEGS R DVN+SIRP G  +  T+VEIKN+N+F  I RAI+ E+ RQ   + 
Sbjct: 177 LDIGDANMQEGSFRVDVNVSIRPKGDEKLYTRVEIKNINSFRFIQRAIELEVERQRDAWE 236

Query: 310 QGKAD-QIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRASLP 368
            G  + +IV ETRL+++  Q+T +MR KE  ADYRYFPEPDL + ++T E ++   + +P
Sbjct: 237 DGTYESEIVQETRLFDQVRQETRSMRGKEEAADYRYFPEPDLLKTVITDEMLEKY-SKIP 295

Query: 369 ELPEAKRRRY-EAMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSDIAAYLK 427
           ELP+ K  R+ +   +       L + + +A YF++++ +G   K A  W+ +++    K
Sbjct: 296 ELPDEKMARFVKDYEMNEYSASVLTSAIEMAHYFESMMEEGVSSKNALTWLTTELQGRFK 355

Query: 428 NEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAKDLVQIT 487
            E ++I++  +  ++LA L+  I+DGTISGK  K++L  L+     V   I    L Q++
Sbjct: 356 GE-INISNSPVDAKKLALLVKRIEDGTISGKAAKDVLDYLMQNSVDVDSAIDTLGLKQVS 414

Query: 488 DPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKILLEKL 546
           D   IE +   V++ N  ++ +Y+SGK KL G+F GQVMK SKG ANP  +N IL  KL
Sbjct: 415 DSGAIEAICDAVIAANGDKVTEYQSGKDKLFGFFVGQVMKESKGSANPQTVNDILKAKL 473


Lambda     K      H
   0.317    0.134    0.379 

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: 38
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: 550
Length of database: 474
Length adjustment: 35
Effective length of query: 515
Effective length of database: 439
Effective search space:   226085
Effective search space used:   226085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_011372963.1 SUDEN_RS06970 (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.1211127.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-182  592.9   0.4   2.2e-182  592.8   0.4    1.0  1  NCBI__GCF_000012965.1:WP_011372963.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011372963.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  592.8   0.4  2.2e-182  2.2e-182       4     480 ..       2     473 ..       1     474 [] 0.98

  Alignments for each domain:
  == domain 1  score: 592.8 bits;  conditional E-value: 2.2e-182
                             TIGR00133   4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 
                                           +e+viGlEvHvqlntk+KlFc+c++++++ k+Ntn+cp cl+lPGalPvlNke+++k ++ ++a+++ i+ ++
  NCBI__GCF_000012965.1:WP_011372963.1   2 FEVVIGLEVHVQLNTKTKLFCSCPTSFNH-KQNTNTCPTCLALPGALPVLNKEVLNKSIMFGTAVDATIN-KT 72 
                                           89**************************9.9*************************************66.6* PP

                             TIGR00133  77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDf 148
                                           s+FdRK YfYpD P++yqitq ++P++e+Gkl+i++e+++ k+i+i+r h+E D+gk+ + +     +s vD+
  NCBI__GCF_000012965.1:WP_011372963.1  73 SYFDRKSYFYPDSPSAYQITQLYTPVVEHGKLRIDFEDGShKTIRINRAHIEADAGKNIHDGA----ISKVDL 141
                                           ***********************************998766*******************965....79**** PP

                             TIGR00133 149 NRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNl 221
                                           NR+g+PLlEiV++Pd++sa+e+  +lkkl++i+ryl+i d++++eGs+RvDvNvsir+kG+ek +trvEiKN+
  NCBI__GCF_000012965.1:WP_011372963.1 142 NRAGTPLLEIVSEPDMRSAEEVTLYLKKLHSIIRYLDIGDANMQEGSFRVDVNVSIRPKGDEKLYTRVEIKNI 214
                                           ************************************************************************* PP

                             TIGR00133 222 nslksiekaieyEieRqkkllkkg...eevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideev 291
                                           ns++ i++aie+E+eRq +++++g   +e++qetr fd+ ++ t s+R Kee++DYRYfpePdl + +i++e+
  NCBI__GCF_000012965.1:WP_011372963.1 215 NSFRFIQRAIELEVERQRDAWEDGtyeSEIVQETRLFDQVRQETRSMRGKEEAADYRYFPEPDLLKTVITDEM 287
                                           ************************99999*******************************************9 PP

                             TIGR00133 292 vkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkk 364
                                           +++    k+pelP++k +r++k+y+++e+ a vl+s  e++++fe++++   ++k+a +W+++el+g+ + + 
  NCBI__GCF_000012965.1:WP_011372963.1 288 LEK--YSKIPELPDEKMARFVKDYEMNEYSASVLTSAIEMAHYFESMMEEGVSSKNALTWLTTELQGRFKGE- 357
                                           988..99**************************************************************987. PP

                             TIGR00133 365 islaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveeviken 437
                                           i+++++ +++++la l+k i++g+is+k+ak++l+ l++n  d+++ i+ lgl q+sd  ++ +i+++vi+ n
  NCBI__GCF_000012965.1:WP_011372963.1 358 INISNSPVDAKKLALLVKRIEDGTISGKAAKDVLDYLMQNSVDVDSAIDTLGLKQVSDSGAIEAICDAVIAAN 430
                                           ************************************************************************* PP

                             TIGR00133 438 pkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            ++v +y+sgk+k+++f+vGqvmk++kg a+p++v+ +lk +l
  NCBI__GCF_000012965.1:WP_011372963.1 431 GDKVTEYQSGKDKLFGFFVGQVMKESKGSANPQTVNDILKAKL 473
                                           ***************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (474 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.51
//
[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