Alignments for a candidate for gatB in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Methylobacterium nodulans ORS 2060

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_015929906.1 MNOD_RS15685 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_000022085.1:WP_015929906.1
          Length = 490

 Score =  408 bits (1049), Expect = e-118
 Identities = 218/473 (46%), Positives = 312/473 (65%), Gaps = 6/473 (1%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E VIG+E+H ++ + SK+FS +   FGAEPN N +++D A PG+LPV+N+  V  A+R 
Sbjct: 18  WEVVIGMEIHAQVTSRSKLFSGASTAFGAEPNDNVSLVDAAMPGMLPVINRECVAQAVRT 77

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121
            + L  +I   S FDRKNYFYPD P+ YQISQ+  PI   G + +++ +GET R+GI RL
Sbjct: 78  GLGLKAQINHRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGEVLVDLPEGETIRVGIERL 137

Query: 122 HMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H    SL  VDLNR G  L+EIVS+PD+RS +EA AY+ KLR+I++Y G 
Sbjct: 138 HLEQDAGKSLHDQHPSLSFVDLNRSGVALMEIVSKPDLRSAEEAKAYVTKLRTILRYLGT 197

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239
            D  ME+G+LR D N+S+R  G E  GT+ E+KN+NS  ++ + +E E +RQ   L  GG
Sbjct: 198 CDGDMEKGNLRADVNVSVRRPG-EFLGTRCEIKNVNSIRFIGQAIEAEARRQIAILEDGG 256

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

Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359
           KA++V E GL AYDA VL   +  +D+FE+ +  G D K  +NW++  +   LNK    +
Sbjct: 317 KARFVAEYGLSAYDATVLVAERASADYFEA-VARGRDGKAAANWVINELFGRLNKEGHGI 375

Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419
            D+ ++ E L  +I LI DGT+S KIAK +F  + ++GG+ + I+E  GL Q++D   + 
Sbjct: 376 EDSPVSAEQLGAIIDLIADGTISGKIAKDLFEIVWSEGGDPRAIVESRGLRQVTDTGAIE 435

Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
             V++ +  N   V      K   +G+ VGQ MKA+ G+ANP  VN LLK +L
Sbjct: 436 AAVDQIIAANPDKVVQ-AQAKPTLLGWFVGQTMKATGGKANPAAVNALLKAKL 487


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: 637
Number of extensions: 31
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: 490
Length adjustment: 34
Effective length of query: 441
Effective length of database: 456
Effective search space:   201096
Effective search space used:   201096
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_015929906.1 MNOD_RS15685 (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.3452236.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-164  534.2   0.0   1.5e-164  533.9   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015929906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015929906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.9   0.0  1.5e-164  1.5e-164       3     480 ..      17     487 ..      16     488 .. 0.97

  Alignments for each domain:
  == domain 1  score: 533.9 bits;  conditional E-value: 1.5e-164
                             TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivse 75 
                                           ++e+viG+E+H q+  +sKlF+ +s+ +   +pN nv+ v+ ++PG lPv+N+e v++A+  +l l+++i+ +
  NCBI__GCF_000022085.1:WP_015929906.1  17 DWEVVIGMEIHAQVTSRSKLFSGASTAFGA-EPNDNVSLVDAAMPGMLPVINRECVAQAVRTGLGLKAQIN-H 87 
                                           5799************************99.**************************************66.6 PP

                             TIGR00133  76 vsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvD 147
                                            svFdRK+YfYpDlP+gyqi+q++ Pi+ +G++ ++l e+e  ++gierlhlE+D+gks + ++  ++ s+vD
  NCBI__GCF_000022085.1:WP_015929906.1  88 RSVFDRKNYFYPDLPQGYQISQYKSPIVGEGEVLVDLPEGEtIRVGIERLHLEQDAGKSLHDQH--PSLSFVD 158
                                           9************************************9988579*****************966..79***** PP

                             TIGR00133 148 fNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220
                                           +NRsgv L+EiV+kPdl+sa+ea+a++ klr+ilryl+  dgd+e+G++R+DvNvs+r    e  gtr EiKN
  NCBI__GCF_000022085.1:WP_015929906.1 159 LNRSGVALMEIVSKPDLRSAEEAKAYVTKLRTILRYLGTCDGDMEKGNLRADVNVSVRRP-GEFLGTRCEIKN 230
                                           **********************************************************55.5789******** PP

                             TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvk 293
                                           +ns++ i +aie E  Rq+++l++g  ++qetr fd +k  t s+R+Kee++DYRYfp+Pdl p+eid+ +++
  NCBI__GCF_000022085.1:WP_015929906.1 231 VNSIRFIGQAIEAEARRQIAILEDGGVIEQETRLFDPNKGETRSMRSKEEAHDYRYFPDPDLLPLEIDDAFID 303
                                           ************************************************************************* PP

                             TIGR00133 294 ekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkis 366
                                           e ++++lpelP++k++r++ eygls++da vlv+++  +d+fe v++  +  k+a+nW+++el g+Lnk+   
  NCBI__GCF_000022085.1:WP_015929906.1 304 E-LKTELPELPDTKKARFVAEYGLSAYDATVLVAERASADYFEAVARGRDG-KAAANWVINELFGRLNKEGHG 374
                                           *.****************************************999887666.********************* PP

                             TIGR00133 367 laeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpk 439
                                           ++++ +++e+l ++i+li +g+is+k+ak+l+e + ++++dp++++e +gl q++d+ ++ ++v+++i+ np+
  NCBI__GCF_000022085.1:WP_015929906.1 375 IEDSPVSAEQLGAIIDLIADGTISGKIAKDLFEIVWSEGGDPRAIVESRGLRQVTDTGAIEAAVDQIIAANPD 447
                                           ************************************************************************* PP

                             TIGR00133 440 evekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           +v + +  k ++l+++vGq mk t g+a+p+ v++llk +l
  NCBI__GCF_000022085.1:WP_015929906.1 448 KVVQAQ-AKPTLLGWFVGQTMKATGGKANPAAVNALLKAKL 487
                                           **9876.5789**************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (490 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: 37.59
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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