GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Herbaspirillum seropedicae SmR1

Align glutamyl-tRNAGln 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.27830.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.84
//
[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:

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:

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:

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:

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