Alignments for a candidate for gatB in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Herbaspirillum seropedicae SmR1

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate HSERO_RS23300 HSERO_RS23300 glutamyl-tRNA amidotransferase subunit B

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



>FitnessBrowser__HerbieS:HSERO_RS23300
          Length = 486

 Score =  459 bits (1180), Expect = e-133
 Identities = 242/484 (50%), Positives = 330/484 (68%), Gaps = 11/484 (2%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M +E VIGLE H +L T+SKIFS SPT FGAE NTQ S +DL  PGVLPVLNK AVE A+
Sbjct: 1   MQWEVVIGLETHTQLSTQSKIFSGSPTRFGAEPNTQASPVDLALPGVLPVLNKGAVERAI 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIE--IEVGGKT--KRI 116
           +  +A+   IA  + F RKNYFYPD PK YQISQF+ P+ + G +   +E  GKT  K I
Sbjct: 61  QFGLAIGATIAPRSIFARKNYFYPDLPKGYQISQFEIPVVQGGTMSFAVEKDGKTEIKTI 120

Query: 117 GITRLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSII 175
            +TR HLEEDAGK  H    G + +D NR GTPL+EIV+EP++R+  EA  Y + L S++
Sbjct: 121 NLTRAHLEEDAGKSLHEDYQGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVGYAKALHSLV 180

Query: 176 QYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQV 235
            + G+ D  M+EGS RCDAN+S+RP+GQE+FGT+ E+KNLNSF F+++ + +E +RQ ++
Sbjct: 181 MWLGICDGNMQEGSFRCDANVSVRPVGQEKFGTRCEIKNLNSFRFLEEAINYEVRRQIEL 240

Query: 236 LLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPE 295
           +  G  + QETR YD   K+T  MR KE + DYRYFP+PDL  L I  EW ERVKA++PE
Sbjct: 241 IEDGGTVVQETRLYDPDKKETRSMRSKEDAQDYRYFPDPDLPPLAISQEWIERVKATMPE 300

Query: 296 LPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGA--EAKQASNWLMGEVSAYL 353
           LP   R+R++ E     YDAMVLT +K MA +FE  V      +AK A+NWLMG+V++ L
Sbjct: 301 LPAAMRERFVAEYALPEYDAMVLTQSKGMASYFEAVVAAAGKEQAKPAANWLMGDVASTL 360

Query: 354 NAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGD----AEKIVKEKG 409
           N E  ++AD  +    LA ++K I  GTIS+KIAK+VF  + E   D    A+ I++ KG
Sbjct: 361 NREDTDIADAPVKAAQLALLLKRIADGTISNKIAKEVFAGMWEARSDKDSLADDIIEAKG 420

Query: 410 LVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKIL 469
           L QISD G L  +V + L  N +S+ +F+ GK++AI  L+GQ MKA++G+ANP  + ++L
Sbjct: 421 LKQISDSGALEAIVDQVLAANEKSVAEFRAGKEQAINALIGQAMKATRGKANPAQLTELL 480

Query: 470 LEEI 473
            +++
Sbjct: 481 RKKL 484


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: 591
Number of extensions: 16
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: 486
Length adjustment: 34
Effective length of query: 442
Effective length of database: 452
Effective search space:   199784
Effective search space used:   199784
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: 51 (24.3 bits)

Align candidate HSERO_RS23300 HSERO_RS23300 (glutamyl-tRNA 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.9775.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-174  565.2   0.0   5.6e-174  565.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS23300  HSERO_RS23300 glutamyl-tRNA amid


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS23300  HSERO_RS23300 glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  565.1   0.0  5.6e-174  5.6e-174       2     480 ..       1     484 [.       1     485 [. 0.96

  Alignments for each domain:
  == domain 1  score: 565.1 bits;  conditional E-value: 5.6e-174
                                  TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalaln 69 
                                                +++e+viGlE+H+ql t+sK+F+ +++++   +pNt+ +pv+l+lPG+lPvlNk av+ A++ +la++
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300   1 MQWEVVIGLETHTQLSTQSKIFSGSPTRFGA-EPNTQASPVDLALPGVLPVLNKGAVERAIQFGLAIG 67 
                                                5789*************************99.************************************ PP

                                  TIGR00133  70 skivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke....keigierlhlEeDtgks 133
                                                +  +++ s+F+RK+YfYpDlPkgyqi+q+++P++++G+++  +e++     k+i+++r hlEeD+gks
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300  68 AT-IAPRSIFARKNYFYPDLPKGYQISQFEIPVVQGGTMSFAVEKDGkteiKTINLTRAHLEEDAGKS 134
                                                **.668*******************************99877666555699***************** PP

                                  TIGR00133 134 qykesdkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvN 201
                                                 ++    + ++ +D+NR+g+PLlEiVt+P+++sa ea+ + k l++++ +l+i dg+++eGs+R+D+N
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 135 LHEDY--QGMTGIDLNRAGTPLLEIVTEPEMRSAAEAVGYAKALHSLVMWLGICDGNMQEGSFRCDAN 200
                                                **944..6899********************************************************* PP

                                  TIGR00133 202 vsirlkGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKe 269
                                                vs+r++Gqek+gtr EiKNlns++ +e+ai+yE+ Rq++l+++g +v+qetr +d  k+ t s+R+Ke
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 201 VSVRPVGQEKFGTRCEIKNLNSFRFLEEAINYEVRRQIELIEDGGTVVQETRLYDPDKKETRSMRSKE 268
                                                ******************************************************************** PP

                                  TIGR00133 270 eseDYRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafee 337
                                                +++DYRYfp+Pdlpp+ i++e++++ v++++pelP a+r+r++ ey l e+da vl++ + ++++fe 
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 269 DAQDYRYFPDPDLPPLAISQEWIER-VKATMPELPAAMRERFVAEYALPEYDAMVLTQSKGMASYFEA 335
                                                ************************9.****************************************** PP

                                  TIGR00133 338 vvklikep..klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleelle 403
                                                vv +++++  k a+nW++ +++++Ln++++++a+a +k+ +la l+k i +g+is+k+ake++  + e
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 336 VVAAAGKEqaKPAANWLMGDVASTLNREDTDIADAPVKAAQLALLLKRIADGTISNKIAKEVFAGMWE 403
                                                **99988766899******************************************************9 PP

                                  TIGR00133 404 n....kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgra 467
                                                      + ++ +ie++gl qisd  +l +iv++v++ n+k+v ++++gke+a++ l+Gq+mk t+g+a
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 404 ArsdkDSLADDIIEAKGLKQISDSGALEAIVDQVLAANEKSVAEFRAGKEQAINALIGQAMKATRGKA 471
                                                955433445778999***************************************************** PP

                                  TIGR00133 468 dpkevekllkell 480
                                                +p++ ++ll+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS23300 472 NPAQLTELLRKKL 484
                                                **********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (486 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: 12.34
//
[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