Alignments for a candidate for gatB in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Clostridium acetobutylicum ATCC 824

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate NP_349276.1 CA_C2669 aspartyl/glutamyl-tRNA amidotransferase subunit B

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



>NCBI__GCF_000008765.1:NP_349276.1
          Length = 476

 Score =  509 bits (1311), Expect = e-149
 Identities = 251/477 (52%), Positives = 343/477 (71%), Gaps = 2/477 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M +E VIGLEVH EL TK+K++      FG + NT    + +G PG LP +NK AV++ +
Sbjct: 1   MEYEIVIGLEVHAELATKTKMYCGCTAEFGGQPNTHVCPVCMGLPGALPHINKRAVDYGI 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119
           KA +ALNC I    + DRK+ FYPDN + YQI+Q + P+  NG+IEIE+  G  K+IG+ 
Sbjct: 61  KAGLALNCSITHIGRMDRKHIFYPDNSRNYQITQDELPLCTNGYIEIELEDGSKKKIGVE 120

Query: 120 RLHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
           R+H+EEDAGKL HT  G +LVDFNR G PL EIVS+PD+R+P EA  YLE+LKSI+   G
Sbjct: 121 RIHIEEDAGKLLHTNAG-TLVDFNRCGVPLAEIVSKPDMRSPREAVTYLEELKSILSCVG 179

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           VSDCKMEEGSLRCDANIS+   G +EFG +TE+KN+NSF  V+K L +E +R  + + SG
Sbjct: 180 VSDCKMEEGSLRCDANISVMKKGAKEFGVRTEIKNMNSFKAVEKALNYEYERHIKAIESG 239

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             + QETRR+D+A  +T  MR KE ++DYRYFPE DLV L IDDEW E ++ +IPELP +
Sbjct: 240 EKLTQETRRWDDAKNETAPMRSKEEANDYRYFPEGDLVTLNIDDEWIESIRKTIPELPYQ 299

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359
           +R+R+I+E G   YDA VLTLT  MADFFE+T +   +AK ASNWLMG++S  +      
Sbjct: 300 KRERFIKEFGIPKYDASVLTLTMSMADFFEKTAKISGDAKSASNWLMGDISKIMKENYVW 359

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           + D+  TPE L+ +IKLI +GT+S+ I KKV  ++ E G   + I++E+GL+Q S+E  +
Sbjct: 360 IEDLKFTPEQLSELIKLINEGTVSNAIGKKVIIKMFETGKSPKNIIEEEGLIQNSNEDEI 419

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKKR 476
           L +V E L  N +SIED+KNGK+R +GFL+G +MK +KG+ANP +VNK++++E+ K+
Sbjct: 420 LNIVKEVLSENEKSIEDYKNGKNRVVGFLIGLVMKKTKGKANPKIVNKLMIDELNKQ 476


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: 670
Number of extensions: 22
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: 476
Length adjustment: 33
Effective length of query: 443
Effective length of database: 443
Effective search space:   196249
Effective search space used:   196249
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 NP_349276.1 CA_C2669 (aspartyl/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.8914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   6.4e-179  581.4   2.2   7.2e-179  581.2   2.2    1.0  1  lcl|NCBI__GCF_000008765.1:NP_349276.1  CA_C2669 aspartyl/glutamyl-tRNA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_349276.1  CA_C2669 aspartyl/glutamyl-tRNA amidotransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.2   2.2  7.2e-179  7.2e-179       2     480 ..       1     473 [.       1     474 [. 0.98

  Alignments for each domain:
  == domain 1  score: 581.2 bits;  conditional E-value: 7.2e-179
                              TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskiv 73 
                                            +eye+viGlEvH  l tk+K++c c+ e+   +pNt+vcpvc+glPGalP +Nk+av   +k +laln+  +
  lcl|NCBI__GCF_000008765.1:NP_349276.1   1 MEYEIVIGLEVHAELATKTKMYCGCTAEFGG-QPNTHVCPVCMGLPGALPHINKRAVDYGIKAGLALNCS-I 70 
                                            69*****************************.9*************************************.5 PP

                              TIGR00133  74 sevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqs 144
                                            +++   dRKh fYpD  ++yqitq +lP++++G++eiele+++ k+ig+er+h+EeD+gk+ +++      +
  lcl|NCBI__GCF_000008765.1:NP_349276.1  71 THIGRMDRKHIFYPDNSRNYQITQDELPLCTNGYIEIELEDGSkKKIGVERIHIEEDAGKLLHTNA----GT 138
                                            57************************************98865499******************66....58 PP

                              TIGR00133 145 lvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrv 216
                                            lvDfNR+gvPL EiV+kPd++s+ ea+ +l++l++il  +++sd+++eeGs+R+D+N+s+  kG +++g r 
  lcl|NCBI__GCF_000008765.1:NP_349276.1 139 LVDFNRCGVPLAEIVSKPDMRSPREAVTYLEELKSILSCVGVSDCKMEEGSLRCDANISVMKKGAKEFGVRT 210
                                            ************************************************************************ PP

                              TIGR00133 217 EiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieid 288
                                            EiKN+ns+k++eka++yE+eR +k++++ge+++qetr +d++k+ t  +R+Kee++DYRYfpe dl++++id
  lcl|NCBI__GCF_000008765.1:NP_349276.1 211 EIKNMNSFKAVEKALNYEYERHIKAIESGEKLTQETRRWDDAKNETAPMRSKEEANDYRYFPEGDLVTLNID 282
                                            ************************************************************************ PP

                              TIGR00133 289 eevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeL 360
                                            +e++++ +++++pelP +kr+r+ ke+g+ ++da vl+  ++++d fe+ +k ++++k a nW++ ++ + +
  lcl|NCBI__GCF_000008765.1:NP_349276.1 283 DEWIES-IRKTIPELPYQKRERFIKEFGIPKYDASVLTLTMSMADFFEKTAKISGDAKSASNWLMGDISKIM 353
                                            *****9.***************************************************************** PP

                              TIGR00133 361 nkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklgliqisdekelvkivee 432
                                            +++ + +++  ++pe+l elikli+eg++s+ ++k+++ +++e++k+pk++ie++gliq s+e+e+ +iv+e
  lcl|NCBI__GCF_000008765.1:NP_349276.1 354 KENYVWIEDLKFTPEQLSELIKLINEGTVSNAIGKKVIIKMFETGKSPKNIIEEEGLIQNSNEDEILNIVKE 425
                                            ************************************************************************ PP

                              TIGR00133 433 vikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                            v++en+k++e+yk+gk+++++fl+G vmkktkg+a+pk v+kl+ + l
  lcl|NCBI__GCF_000008765.1:NP_349276.1 426 VLSENEKSIEDYKNGKNRVVGFLIGLVMKKTKGKANPKIVNKLMIDEL 473
                                            ******************************************997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (476 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.37
//
[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