Alignments for a candidate for gatB in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Paraburkholderia phymatum STM815

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012399480.1 BPHY_RS00275 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000020045.1:WP_012399480.1
          Length = 491

 Score =  447 bits (1150), Expect = e-130
 Identities = 235/486 (48%), Positives = 331/486 (68%), Gaps = 15/486 (3%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLE H +L T SKIFS + T FGA  NTQ   +DL  PGVLPV+NK AVE A++ 
Sbjct: 5   WEVVIGLETHAQLSTVSKIFSGAATQFGAAPNTQACPVDLALPGVLPVMNKGAVERAIQF 64

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-----GGKT---K 114
            +A++  IA  + F RKNYFYPD PK YQISQ++ P+ + G I I+V      GK    K
Sbjct: 65  GLAIDATIAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEKAGKEAYEK 124

Query: 115 RIGITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKS 173
            I +TR HLEEDAGK  H    G + +D NR GTPL+EIV+EP++R+  EA AY + L  
Sbjct: 125 TINLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHG 184

Query: 174 IIQYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQE 233
           ++ + G+ D  M+EGS RCDAN+S+RP+GQ+EFGT+ E+KNLNSF F+++ +++E +RQ 
Sbjct: 185 LVVWLGICDGNMQEGSFRCDANVSVRPVGQKEFGTRAEIKNLNSFRFLEEAIQYEVRRQI 244

Query: 234 QVLLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASI 293
           +++  G  + QETR YD   ++T  MR KE + DYRYFP+PDL+ L ID  W ERVK  +
Sbjct: 245 ELIEDGGTVVQETRLYDPDKRETRSMRSKEDAHDYRYFPDPDLMPLVIDASWVERVKGEL 304

Query: 294 PELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQK--GAEAKQASNWLMGEVSA 351
           PELP   +KR++++ G   YDA V+T  K MA ++E  V K   A+AK A+NWLMGEVS+
Sbjct: 305 PELPAAMQKRFVDQYGLTPYDAGVVTAGKAMAAYYEAVVAKVGAAQAKVAANWLMGEVSS 364

Query: 352 YLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGD----AEKIVKE 407
            LN E  ++AD  ++   LA +++ I  GTIS+KIAK++F  + E+       A++I++ 
Sbjct: 365 QLNREGLDIADSPVSAAQLALVLQRIADGTISNKIAKEIFLAIWEEKATDEAAADRIIEA 424

Query: 408 KGLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNK 467
           KGL QISD G L  ++ E L  N +S+E+F+ GK++A   L+GQ MKA+KG+ANP  VN+
Sbjct: 425 KGLKQISDTGALEAIIDEVLAANQKSVEEFRAGKEKAFNALIGQAMKATKGKANPQQVNE 484

Query: 468 ILLEEI 473
           +L +++
Sbjct: 485 LLKKKL 490


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: 572
Number of extensions: 14
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: 491
Length adjustment: 34
Effective length of query: 442
Effective length of database: 457
Effective search space:   201994
Effective search space used:   201994
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_012399480.1 BPHY_RS00275 (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.3594521.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-174  565.8   0.0   3.9e-174  565.6   0.0    1.0  1  NCBI__GCF_000020045.1:WP_012399480.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020045.1:WP_012399480.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.6   0.0  3.9e-174  3.9e-174       2     480 ..       3     490 ..       2     491 .] 0.97

  Alignments for each domain:
  == domain 1  score: 565.6 bits;  conditional E-value: 3.9e-174
                             TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivs 74 
                                           +++e+viGlE+H ql t sK+F+ + +++    pNt+ cpv+l+lPG+lPv+Nk av+ A++ +la+++  ++
  NCBI__GCF_000020045.1:WP_012399480.1   3 TQWEVVIGLETHAQLSTVSKIFSGAATQFGA-APNTQACPVDLALPGVLPVMNKGAVERAIQFGLAIDAT-IA 73 
                                           5789*************************99.9*************************************.66 PP

                             TIGR00133  75 evsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke........keigierlhlEeDtgksqykesd 139
                                           + s+F+RK+YfYpDlPkgyqi+q+++P++++G+++i++ ++e        k+i+++r hlEeD+gks ++   
  NCBI__GCF_000020045.1:WP_012399480.1  74 PRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQITIQVPANEkagkeayeKTINLTRAHLEEDAGKSLHED-- 144
                                           8************************************9998889999**********************94.. PP

                             TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqeke 212
                                            + ++ +D+NR+g+PLlEiVt+P+++sa ea+a+ k l+ ++ +l+i dg+++eGs+R+D+Nvs+r++Gq+++
  NCBI__GCF_000020045.1:WP_012399480.1 145 FAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKALHGLVVWLGICDGNMQEGSFRCDANVSVRPVGQKEF 217
                                           4789********************************************************************* PP

                             TIGR00133 213 gtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppi 285
                                           gtr+EiKNlns++ +e+ai+yE+ Rq++l+++g +v+qetr +d  k  t s+R+Ke+++DYRYfp+Pdl+p+
  NCBI__GCF_000020045.1:WP_012399480.1 218 GTRAEIKNLNSFRFLEEAIQYEVRRQIELIEDGGTVVQETRLYDPDKRETRSMRSKEDAHDYRYFPDPDLMPL 290
                                           ************************************************************************* PP

                             TIGR00133 286 eideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep..klavnWileel 356
                                           +id ++v++ v+++lpelP a+++r++ +ygl  +da v+++ + ++ ++e vv  ++ +  k a+nW++ e+
  NCBI__GCF_000020045.1:WP_012399480.1 291 VIDASWVER-VKGELPELPAAMQKRFVDQYGLTPYDAGVVTAGKAMAAYYEAVVAKVGAAqaKVAANWLMGEV 362
                                           ********9.******************************************9988776656999******** PP

                             TIGR00133 357 lgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen....kkdpkklieklgliqisdeke 425
                                            ++Ln++ +++a++ +++ +la +++ i +g+is+k+ake++  + e+    +  ++++ie++gl qisd+ +
  NCBI__GCF_000020045.1:WP_012399480.1 363 SSQLNREGLDIADSPVSAAQLALVLQRIADGTISNKIAKEIFLAIWEEkatdEAAADRIIEAKGLKQISDTGA 435
                                           ******************************************999999777677899**************** PP

                             TIGR00133 426 lvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                           l +i++ev++ n+k+ve++++gkeka++ l+Gq+mk tkg+a+p++v++llk++l
  NCBI__GCF_000020045.1:WP_012399480.1 436 LEAIIDEVLAANQKSVEEFRAGKEKAFNALIGQAMKATKGKANPQQVNELLKKKL 490
                                           ****************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (491 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.60
//
[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