Alignments for a candidate for gatB in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Burkholderia phytofirmans PsJN

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate BPHYT_RS01560 BPHYT_RS01560 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

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



>FitnessBrowser__BFirm:BPHYT_RS01560
          Length = 491

 Score =  442 bits (1136), Expect = e-128
 Identities = 229/486 (47%), Positives = 329/486 (67%), Gaps = 15/486 (3%)

Query: 3   FETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMKA 62
           +E VIGLE H +L T+SKIFS + T FGA  NTQ S +DL  PG LPV+N+ AVE A++ 
Sbjct: 5   WEVVIGLETHAQLSTQSKIFSGTATQFGAAPNTQASPVDLALPGTLPVMNRGAVERAIQF 64

Query: 63  AMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKR------- 115
            +A+   +A  + F RKNYFYPD PK YQISQ++ P+ + G + I+V    K        
Sbjct: 65  GLAIGATVAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQVTIQVPANEKAGKEAYEK 124

Query: 116 -IGITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKS 173
            + +TR HLEEDAGK  H    G + +D NR GTPL+EIV+EP++R+  EA AY + L +
Sbjct: 125 VVNLTRAHLEEDAGKSLHEDFAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKTLHT 184

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

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

Query: 294 PELPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQK--GAEAKQASNWLMGEVSA 351
            ELP   ++R++ + G   YDA VLT +K MA ++E  V K   A AK A+NWLMGEVS+
Sbjct: 305 TELPVAIQQRFVSQYGLTPYDANVLTSSKAMAAYYEAVVSKVGPANAKVAANWLMGEVSS 364

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

Query: 408 KGLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNK 467
           KGL QISD G L  ++ E L  NP+S+E+F+ GK++A   L+GQ MKA+KG+ANP  VN+
Sbjct: 425 KGLKQISDTGALEAIIDEVLAANPKSVEEFRAGKEKAFNALIGQAMKATKGKANPAQVNE 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: 561
Number of extensions: 13
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 BPHYT_RS01560 BPHYT_RS01560 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase 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.27548.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-174  566.6   0.0   2.3e-174  566.4   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS01560  BPHYT_RS01560 aspartyl/glutamyl-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS01560  BPHYT_RS01560 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  566.4   0.0  2.3e-174  2.3e-174       3     480 ..       4     490 ..       2     491 .] 0.98

  Alignments for each domain:
  == domain 1  score: 566.4 bits;  conditional E-value: 2.3e-174
                                TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 
                                              ++e+viGlE+H ql t+sK+F+ + +++    pNt+ +pv+l+lPG+lPv+N+ av+ A++ +la+++  
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560   4 QWEVVIGLETHAQLSTQSKIFSGTATQFGA-APNTQASPVDLALPGTLPVMNRGAVERAIQFGLAIGAT- 71 
                                              689*************************99.9************************************9. PP

                                TIGR00133  73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke........keigierlhlEeDtgksq 134
                                              v++ s+F+RK+YfYpDlPkgyqi+q+++P++++G+++i++ ++e        k ++++r hlEeD+gks 
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560  72 VAPRSIFARKNYFYPDLPKGYQISQYEIPVVQGGQVTIQVPANEkagkeayeKVVNLTRAHLEEDAGKSL 141
                                              678************************************9998889999**9****************** PP

                                TIGR00133 135 ykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsi 204
                                              ++    + ++ +D+NR+g+PLlEiVt+P+++sa ea+a+ k l++++ +l+i dg+++eGs+R+D+Nvs+
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 142 HED--FAGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVAYAKTLHTLVTWLGICDGNMQEGSFRCDANVSV 209
                                              *94..4789************************************************************* PP

                                TIGR00133 205 rlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDY 274
                                              r++Gq ++gtr+EiKNlns++ +e+ai+yE+ Rq++l+++g +v+qetr +d  k  t s+R+Ke+++DY
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 210 RPVGQAEFGTRAEIKNLNSFRFLEEAIQYEVRRQIELIEDGGTVVQETRLYDPDKRETRSMRSKEDAHDY 279
                                              ********************************************************************** PP

                                TIGR00133 275 RYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                              RYfp+Pdl+p++id  ++++ v+++++elP a ++r++++ygl  +da+vl+s + ++ ++e vv+ +++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 280 RYFPDPDLMPLVIDAAWIER-VKAEMTELPVAIQQRFVSQYGLTPYDANVLTSSKAMAAYYEAVVSKVGP 348
                                              *******************9.*********************************************9988 PP

                                TIGR00133 345 p..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen....kkdp 408
                                              +  k a+nW++ e+ ++Ln++ +++ae+ +++ +la l++ i +g+is+k+ake++  + e+    ++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 349 AnaKVAANWLMGEVSSQLNREGLDIAENPVSSAQLALLLQRIADGTISNKIAKEIFLAIWEEkatdESAA 418
                                              76799***************************************************99999977777889 PP

                                TIGR00133 409 kklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllke 478
                                              +++ie++gl qisd+ +l +i++ev++ npk+ve++++gkeka++ l+Gq+mk tkg+a+p++v++llk+
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 419 DRIIEAKGLKQISDTGALEAIIDEVLAANPKSVEEFRAGKEKAFNALIGQAMKATKGKANPAQVNELLKK 488
                                              9********************************************************************* PP

                                TIGR00133 479 ll 480
                                              +l
  lcl|FitnessBrowser__BFirm:BPHYT_RS01560 489 KL 490
                                              98 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.55
//
[ok]

This GapMind analysis is from Apr 09 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