Alignments for a candidate for gatB in Methylocapsa aurea KYG T

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylocapsa aurea KYG T

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_036259399.1 DL86_RS06300 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000746085.1:WP_036259399.1
          Length = 516

 Score =  399 bits (1024), Expect = e-115
 Identities = 214/499 (42%), Positives = 306/499 (61%), Gaps = 31/499 (6%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           FE VIG+E+H ++ + SK+FS +   FG EPN+N +++D A PG+LPV+N+  V  A+R 
Sbjct: 18  FEVVIGMEIHAQVTSRSKLFSGASTVFGNEPNANVSLVDAAMPGMLPVINEECVAQAIRT 77

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDG-ETKRIGITRL 121
            + L  +I   S FDRKNYFYPD P+ YQISQ+  PI   G + ++V   E   +GI RL
Sbjct: 78  GLGLEAQINLRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGVVIVDVSPTEQIEVGIERL 137

Query: 122 HMEEDAGKSTH--KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H      S VDLNR G  L+EIVS+PD+RS  EA AY+ KLR+I++Y G 
Sbjct: 138 HLEQDAGKSLHDQSATESFVDLNRSGVALMEIVSKPDMRSSDEARAYVTKLRTILRYIGS 197

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
            D  ME+GSLR D N+S+R  G E  GT+ E+KN+NS  ++ + +E E +RQ   +  GG
Sbjct: 198 CDGNMEQGSLRADVNVSVRRPG-EPLGTRCEIKNVNSIRFIAQAIEVEARRQIGIIEDGG 256

Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299
           +I QETR FD   G+T  MR KE + DYRYFP+PD++PL  D  + + ++  +PELPD +
Sbjct: 257 KIDQETRLFDPVRGETRSMRSKEEAHDYRYFPDPDLLPLEFDQDYVDALKAELPELPDAK 316

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGA---DVKLTSNWLMGGVNEYLNKNQ 356
           KA+++ + GLPAYDA VL   KE +D++E+ ++ G    D KL +NW+ G V  Y N   
Sbjct: 317 KARFIKDYGLPAYDAGVLVADKETADYYEAAVKFGGASRDAKLVANWISGDVAAYANTQG 376

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVF--------------------PELAAK 396
           + +  T + P  +AG++ LI DGT+S KIAK V                      + AA 
Sbjct: 377 LSVAQTHIRPGQIAGIVDLIADGTISGKIAKDVLAIIIAEDKDRVSGSLSAIEGSDTAAM 436

Query: 397 GGNA---KQIMEDNGLVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMK 453
            G+    + I+E  G+ Q++D   +   V+  +  N   V      K   +G+ VGQ+MK
Sbjct: 437 SGSVSDPRAIVEARGMKQVTDTGAIAAAVDAIIAANPDKVAQ-AQAKPSMLGWFVGQVMK 495

Query: 454 ASKGQANPQLVNQLLKQEL 472
            + G+ANPQ VN+LLK +L
Sbjct: 496 ETGGKANPQAVNELLKSKL 514


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: 630
Number of extensions: 34
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: 516
Length adjustment: 34
Effective length of query: 441
Effective length of database: 482
Effective search space:   212562
Effective search space used:   212562
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_036259399.1 DL86_RS06300 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
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.31587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-161  521.9   0.0   7.9e-161  521.7   0.0    1.0  1  lcl|NCBI__GCF_000746085.1:WP_036259399.1  DL86_RS06300 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000746085.1:WP_036259399.1  DL86_RS06300 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.7   0.0  7.9e-161  7.9e-161       3     480 ..      17     514 ..      15     515 .. 0.97

  Alignments for each domain:
  == domain 1  score: 521.7 bits;  conditional E-value: 7.9e-161
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e+viG+E+H q+  +sKlF+ +s+ + + +pN nv+ v+ ++PG lPv+N+e v++A+  +l l+++
  lcl|NCBI__GCF_000746085.1:WP_036259399.1  17 DFEVVIGMEIHAQVTSRSKLFSGASTVFGN-EPNANVSLVDAAMPGMLPVINEECVAQAIRTGLGLEAQ 84 
                                               79****************************.************************************** PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139
                                               i+   svFdRK+YfYpDlP+gyqi+q++ Pi+ +G++ ++++ +e  e+gierlhlE+D+gks + +s 
  lcl|NCBI__GCF_000746085.1:WP_036259399.1  85 IN-LRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGVVIVDVSPTEqIEVGIERLHLEQDAGKSLHDQSA 152
                                               77.59**********************************998777369******************775 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                 + s+vD+NRsgv L+EiV+kPd++s++eara++ klr+ilry++  dg++e+Gs+R+DvNvs+r   
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 153 --TESFVDLNRSGVALMEIVSKPDMRSSDEARAYVTKLRTILRYIGSCDGNMEQGSLRADVNVSVRRP- 218
                                               ..79**************************************************************55. PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                                e  gtr EiKN+ns++ i++aie E  Rq+ ++++g ++ qetr fd  +  t s+R+Kee++DYRYf
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 219 GEPLGTRCEIKNVNSIRFIAQAIEVEARRQIGIIEDGGKIDQETRLFDPVRGETRSMRSKEEAHDYRYF 287
                                               5789***************************************************************** PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep. 345
                                               p+Pdl p+e+d+++v+  ++++lpelP+ak++r+ k+ygl ++da vlv+d+e +d++e +vk  + + 
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 288 PDPDLLPLEFDQDYVDA-LKAELPELPDAKKARFIKDYGLPAYDAGVLVADKETADYYEAAVKFGGASr 355
                                               ****************9.9*******************************************9876655 PP

                                 TIGR00133 346 ..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen........ 404
                                                 kl++nWi  +++++ n++ +s+a++ ++p ++a +++li +g+is+k+ak++l  ++ +        
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 356 daKLVANWISGDVAAYANTQGLSVAQTHIRPGQIAGIVDLIADGTISGKIAKDVLAIIIAEdkdrvsgs 424
                                               66*********************************************************999******* PP

                                 TIGR00133 405 ...............kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGq 458
                                                               +dp++++e++g+ q++d+ ++ ++v+++i+ np++v + +  k ++l+++vGq
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 425 lsaiegsdtaamsgsVSDPRAIVEARGMKQVTDTGAIAAAVDAIIAANPDKVAQAQ-AKPSMLGWFVGQ 492
                                               *************9999***********************************9865.6789******** PP

                                 TIGR00133 459 vmkktkgradpkevekllkell 480
                                               vmk+t g+a+p+ v++llk +l
  lcl|NCBI__GCF_000746085.1:WP_036259399.1 493 VMKETGGKANPQAVNELLKSKL 514
                                               *******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (516 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: 00:00:00.03
# Mc/sec: 7.78
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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