Alignments for a candidate for gatB in Rhizobium leguminosarum 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Rhizobium leguminosarum 3841

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_011651687.1 RL_RS10805 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000009265.1:WP_011651687.1
          Length = 500

 Score =  407 bits (1047), Expect = e-118
 Identities = 215/478 (44%), Positives = 310/478 (64%), Gaps = 11/478 (2%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E ++G+EVH ++ ++SK+FS +   FG   NSN +++D A PG+LPV+N+  V  A+R 
Sbjct: 22  WEVIVGMEVHAQVLSNSKLFSGASTEFGKPQNSNVSMVDAAMPGMLPVINEECVKQAVRT 81

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETK------RI 116
            + L  +I   S FDRKNYFYPD P+ YQISQF  PI   G I I +  + +       I
Sbjct: 82  GLGLKAQINKRSLFDRKNYFYPDLPQGYQISQFKDPIVGEGKIVISLGPDRQGQFEDIEI 141

Query: 117 GITRLHMEEDAGKSTHK--GEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSII 174
           GI RLH+E+DAGKS H      S VDLNR G  L+EIVS+PD+RS  EA AY+ KLRSI+
Sbjct: 142 GIERLHLEQDAGKSMHDQHATMSYVDLNRSGVALMEIVSKPDMRSSDEAKAYMTKLRSIV 201

Query: 175 QYTGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEE 234
           +Y G  D  M+EGS+R D N+S+R  G++ FGT+ E+KN+NS  ++ + +EYE +RQ   
Sbjct: 202 RYLGTCDGNMDEGSMRADVNVSVRRPGED-FGTRCEIKNVNSIRFIGQAIEYEARRQIGI 260

Query: 235 LLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPE 294
           L  GG+I QETR FD + G+T  MR KE + DYRYFP+PD++PL  DDA+ + +   +PE
Sbjct: 261 LEDGGKIDQETRLFDPNKGETRSMRSKEDAHDYRYFPDPDLLPLEFDDAFIKALEADLPE 320

Query: 295 LPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNK 354
           LPD++K ++V ELGL  YDA VL   K ++D+FE+ +  G D K  +NW++  +   LN+
Sbjct: 321 LPDDKKERFVRELGLSIYDASVLVSEKAIADYFEA-VAAGRDGKTAANWVINDLLGALNR 379

Query: 355 NQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISD 414
              ++  T ++P  L  +I LI+ GT+S KIAK +F  + A+GG+  +I+E  G+ Q++D
Sbjct: 380 TGKDIEQTPVSPAQLGAIIDLIKAGTISGKIAKDLFEIVLAEGGDPAEIVEARGMKQVTD 439

Query: 415 EATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
              + K V+E +  N   VE  K  K     + VGQ+MKA+ G+ANPQ V  L+K +L
Sbjct: 440 TGAIEKAVDEIIAANPDQVEKVK-AKPTMAAWFVGQVMKATGGKANPQAVQALVKAKL 496


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: 674
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: 475
Length of database: 500
Length adjustment: 34
Effective length of query: 441
Effective length of database: 466
Effective search space:   205506
Effective search space used:   205506
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_011651687.1 RL_RS10805 (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.9021.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-168  545.5   0.0   5.7e-168  545.3   0.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011651687.1  RL_RS10805 Asp-tRNA(Asn)/Glu-tRN


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011651687.1  RL_RS10805 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 !  545.3   0.0  5.7e-168  5.7e-168       3     480 ..      21     496 ..      19     497 .. 0.96

  Alignments for each domain:
  == domain 1  score: 545.3 bits;  conditional E-value: 5.7e-168
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e+++G+EvH q+  +sKlF+ +s+e+ + ++N+nv+ v+ ++PG lPv+N+e vk+A+  +l l+++
  lcl|NCBI__GCF_000009265.1:WP_011651687.1  21 DWEVIVGMEVHAQVLSNSKLFSGASTEFGK-PQNSNVSMVDAAMPGMLPVINEECVKQAVRTGLGLKAQ 88 
                                               6799*************************9.99************************************ PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke......keigierlhlEeDtgksq 134
                                               i+ + s FdRK+YfYpDlP+gyqi+q++ Pi+ +Gk+ i+l  +        eigierlhlE+D+gks+
  lcl|NCBI__GCF_000009265.1:WP_011651687.1  89 IN-KRSLFDRKNYFYPDLPQGYQISQFKDPIVGEGKIVISLGPDRqgqfedIEIGIERLHLEQDAGKSM 156
                                               66.69**********************************99876667777789**************** PP

                                 TIGR00133 135 ykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvs 203
                                               + ++  +++s+vD+NRsgv L+EiV+kPd++s++ea+a++ klr+i+ryl+  dg+++eGsmR+DvNvs
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 157 HDQH--ATMSYVDLNRSGVALMEIVSKPDMRSSDEAKAYMTKLRSIVRYLGTCDGNMDEGSMRADVNVS 223
                                               *977..58************************************************************* PP

                                 TIGR00133 204 irlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeese 272
                                               +r    e++gtr EiKN+ns++ i +aieyE  Rq+ +l++g ++ qetr fd +k  t s+R+Ke+++
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 224 VRRP-GEDFGTRCEIKNVNSIRFIGQAIEYEARRQIGILEDGGKIDQETRLFDPNKGETRSMRSKEDAH 291
                                               **55.6789************************************************************ PP

                                 TIGR00133 273 DYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkl 341
                                               DYRYfp+Pdl p+e+d+ ++k  +e+ lpelP+ k++r+++e+gls +da vlvs++ ++d+fe v+  
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 292 DYRYFPDPDLLPLEFDDAFIKA-LEADLPELPDDKKERFVRELGLSIYDASVLVSEKAIADYFEAVAAG 359
                                               *********************9.****************************************988765 PP

                                 TIGR00133 342 ikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkk 410
                                                +  k+a+nW++++llg Ln++  +++++ ++p +l ++i+lik+g+is+k+ak+l+e +l +++dp +
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 360 RD-GKTAANWVINDLLGALNRTGKDIEQTPVSPAQLGAIIDLIKAGTISGKIAKDLFEIVLAEGGDPAE 427
                                               55.5***************************************************************** PP

                                 TIGR00133 411 lieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkel 479
                                               ++e++g+ q++d+ ++ k+v+e+i+ np++vek k+ k ++  ++vGqvmk t g+a+p+ v++l+k +
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 428 IVEARGMKQVTDTGAIEKAVDEIIAANPDQVEKVKA-KPTMAAWFVGQVMKATGGKANPQAVQALVKAK 495
                                               ********************************9976.56788999*********************988 PP

                                 TIGR00133 480 l 480
                                               l
  lcl|NCBI__GCF_000009265.1:WP_011651687.1 496 L 496
                                               7 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.95
//
[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