Alignments for a candidate for gatB in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Heliobacterium modesticaldum Ice1; ATCC 51547

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012284006.1 HM1_RS13770 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

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



>NCBI__GCF_000019165.1:WP_012284006.1
          Length = 501

 Score =  561 bits (1446), Expect = e-164
 Identities = 282/495 (56%), Positives = 367/495 (74%), Gaps = 21/495 (4%)

Query: 2   NFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAMK 61
           +FE V+GLEVHVEL TKSKIF    T FG E N+    + LG PGVLPVLN++ V++AMK
Sbjct: 6   DFEIVMGLEVHVELHTKSKIFCGCTTEFGGEQNSHVCPVCLGLPGVLPVLNRQVVDYAMK 65

Query: 62  AAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVGGKTKRIGITRL 121
           A +ALNCEIA  +KFDRKNYFYPD PKAYQISQ+D PI +NG+IEIE GGK KRIGITR+
Sbjct: 66  AGLALNCEIAEFSKFDRKNYFYPDLPKAYQISQYDLPIAKNGYIEIEAGGKQKRIGITRV 125

Query: 122 HLEEDAGKLTH------TGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSII 175
           H+EEDAGKL H      +G  YSL D+NR G PL+EIVSEPDIR+ EEA AYLE+LK+I+
Sbjct: 126 HMEEDAGKLVHAGAVNLSGADYSLADYNRTGVPLIEIVSEPDIRSIEEAIAYLEQLKAIL 185

Query: 176 QYTGVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQV 235
           +YT VSDCKME+GSLRCDAN+SLRP GQ+EFGT+TELKN+NSF  +Q+ LE+E +RQ ++
Sbjct: 186 EYTEVSDCKMEQGSLRCDANVSLRPWGQKEFGTRTELKNMNSFKALQRALEYEIERQAEI 245

Query: 236 LLSGFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPE 295
           L  G  + QETR +DEA   TI +R KE + DYRYFP+PDLV L I  EW ++V+ ++PE
Sbjct: 246 LREGGAVVQETRMWDEAKGMTISLRSKEEAHDYRYFPDPDLVPLVISREWVDKVRRTLPE 305

Query: 296 LPDERRKRYIEELGFAAYDAMVLTLTKEMADFFEE-------TVQKGAE--------AKQ 340
           LP  RR R I+  G   YDA ++  +K MAD+F+         V  G E        AKQ
Sbjct: 306 LPQARRARLIQSYGLPRYDADIIVSSKAMADYFDAACAAYGIAVPAGTEADGKAKERAKQ 365

Query: 341 ASNWLMGEVSAYLNAEQKELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGD 400
            SN++MGE++ +LNA +K   D  ++P+ L G+++L+E+GTIS+KIAK VF+E+   G  
Sbjct: 366 ISNYMMGELTRFLNASEKGFQDSPISPDNLVGLLRLLEEGTISTKIAKTVFEEMFATGKA 425

Query: 401 AEKIVKEKGLVQISDEGVLLKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQA 460
           A+ +V+EKGLVQISDEG +  +++E +  NP  + D+K GK++A+GFLVGQ MKA+KG+A
Sbjct: 426 AKTVVEEKGLVQISDEGAIASVISEIVAANPSVVADYKAGKEKAMGFLVGQAMKATKGKA 485

Query: 461 NPPMVNKILLEEIKK 475
           NP +VNK+L EE+ K
Sbjct: 486 NPGLVNKLLKEELAK 500


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: 725
Number of extensions: 33
Number of successful extensions: 3
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: 501
Length adjustment: 34
Effective length of query: 442
Effective length of database: 467
Effective search space:   206414
Effective search space used:   206414
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_012284006.1 HM1_RS13770 (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.9730.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-186  606.8   0.0   1.5e-186  606.5   0.0    1.1  1  lcl|NCBI__GCF_000019165.1:WP_012284006.1  HM1_RS13770 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012284006.1  HM1_RS13770 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.5   0.0  1.5e-186  1.5e-186       3     480 ..       6     498 ..       4     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 606.5 bits;  conditional E-value: 1.5e-186
                                 TIGR00133   3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 
                                               ++e+v+GlEvHv l tksK+Fc c++e+   ++N++vcpvclglPG+lPvlN+++v  A+k +laln++
  lcl|NCBI__GCF_000019165.1:WP_012284006.1   6 DFEIVMGLEVHVELHTKSKIFCGCTTEFGG-EQNSHVCPVCLGLPGVLPVLNRQVVDYAMKAGLALNCE 73 
                                               79****************************.9************************************* PP

                                 TIGR00133  72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140
                                                ++e+s+FdRK+YfYpDlPk+yqi+q+dlPia++G++eie  +k+k+igi+r+h+EeD+gk+++++  +
  lcl|NCBI__GCF_000019165.1:WP_012284006.1  74 -IAEFSKFDRKNYFYPDLPKAYQISQYDLPIAKNGYIEIEAGGKQKRIGITRVHMEEDAGKLVHAGAVN 141
                                               .668*************************************************************9887 PP

                                 TIGR00133 141 ...dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirl 206
                                                  +++sl D+NR+gvPL+EiV++Pd++s++ea a+l++l++il+y+e+sd+++e+Gs+R+D+Nvs+r+
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 142 lsgADYSLADYNRTGVPLIEIVSEPDIRSIEEAIAYLEQLKAILEYTEVSDCKMEQGSLRCDANVSLRP 210
                                               7789***************************************************************** PP

                                 TIGR00133 207 kGqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275
                                                Gq+++gtr E+KN+ns+k++++a+eyEieRq ++l++g  v+qetr++de+k +t+slR+Kee++DYR
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 211 WGQKEFGTRTELKNMNSFKALQRALEYEIERQAEILREGGAVVQETRMWDEAKGMTISLRSKEEAHDYR 279
                                               ********************************************************************* PP

                                 TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklike 344
                                               Yfp+Pdl+p++i+ e+v++ v+ +lpelP+a+r+rl + ygl  +da ++vs + ++d+f+ +  + + 
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 280 YFPDPDLVPLVISREWVDK-VRRTLPELPQARRARLIQSYGLPRYDADIIVSSKAMADYFDAACAAYGI 347
                                               ******************9.*****************************************99877665 PP

                                 TIGR00133 345 p...............klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakell 398
                                               +               k+  n+++ el++ Ln+++  ++++ ++p++l+ l++l++eg+is k+ak+++
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 348 AvpagteadgkakeraKQISNYMMGELTRFLNASEKGFQDSPISPDNLVGLLRLLEEGTISTKIAKTVF 416
                                               55578888999998889999************************************************* PP

                                 TIGR00133 399 eellenkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgra 467
                                               ee++ ++k +k+++e++gl+qisde ++ +++ e+++ np  v +yk+gkeka++flvGq+mk tkg+a
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 417 EEMFATGKAAKTVVEEKGLVQISDEGAIASVISEIVAANPSVVADYKAGKEKAMGFLVGQAMKATKGKA 485
                                               ********************************************************************* PP

                                 TIGR00133 468 dpkevekllkell 480
                                               +p  v+kllke l
  lcl|NCBI__GCF_000019165.1:WP_012284006.1 486 NPGLVNKLLKEEL 498
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (501 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: 8.80
//
[ok]

This GapMind analysis is from Apr 10 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