Alignments for a candidate for gatB in Clostridium kluyveri DSM 555

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Clostridium kluyveri DSM 555

Align glutamyl-tRNA^Gln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate WP_012103792.1 CKL_RS16885 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B

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



>NCBI__GCF_000016505.1:WP_012103792.1
          Length = 476

 Score =  464 bits (1194), Expect = e-135
 Identities = 233/476 (48%), Positives = 327/476 (68%), Gaps = 2/476 (0%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M FE VIGLEVHVEL T++KI+    T FG+E N     + LG PG LP LNK+ VE+A+
Sbjct: 1   MEFEAVIGLEVHVELLTETKIYCGCSTAFGSEPNKHVCPVCLGLPGSLPRLNKKVVEYAI 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEVG-GKTKRIGIT 119
           KA +ALNC I   ++ DRKNYFY D PK YQI+Q + PI   G+IEI    G+ KRIGI 
Sbjct: 61  KAGLALNCSINNKSRMDRKNYFYADCPKNYQITQQEIPICREGFIEIRNHLGEKKRIGIE 120

Query: 120 RLHLEEDAGKLTHTGDGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYTG 179
           R+H+EEDAGKL HT +G +L+D+NR G PL+EIVS+PDIRT +EA +YLE L++I+++ G
Sbjct: 121 RIHMEEDAGKLIHTDEG-TLIDYNRAGIPLIEIVSKPDIRTSKEAVSYLEDLRNILKFIG 179

Query: 180 VSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLSG 239
           VSDCKME+GSLRCD NIS+RP    + G KTE+KN+NSF  ++K +++E KRQ  ++ SG
Sbjct: 180 VSDCKMEQGSLRCDCNISIRPKHNLKLGVKTEIKNMNSFKALEKAIQYEYKRQSDLIESG 239

Query: 240 FFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPDE 299
             ++QETRR+++A   T +MR KE ++DYRYFPE DL  + I D + + ++ +IPELPD+
Sbjct: 240 EKVRQETRRWNDAKNVTEVMRSKEYANDYRYFPEGDLTAINISDNYIDNIRKTIPELPDK 299

Query: 300 RRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQKE 359
           +  R++EE   +  +  +L L  E+ DFFE   +   + K  SNW+ G++S         
Sbjct: 300 KIDRFVEEFKISRKEIEILILNMEIGDFFENAAKLSGDPKSVSNWITGDISRLAKETGIP 359

Query: 360 LADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDAEKIVKEKGLVQISDEGVL 419
           L ++  T   LA +I+ I  G IS+ I KKV +E+  KG    +I+ EKG VQ S +  +
Sbjct: 360 LNNLNFTERDLAELIEFINCGVISNNIGKKVIEEMFYKGKSPRQIIHEKGFVQNSSKEKI 419

Query: 420 LKLVTEALDNNPQSIEDFKNGKDRAIGFLVGQIMKASKGQANPPMVNKILLEEIKK 475
           LK+V E ++ NP+SIED+K GK +A+ F++G +MK +KG ANP +VNK++ EEI K
Sbjct: 420 LKVVKEVMEENPKSIEDYKKGKKKAVKFMIGMVMKKTKGNANPMLVNKLVEEEIGK 475


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: 648
Number of extensions: 36
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 WP_012103792.1 CKL_RS16885 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB 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.23813.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     6e-180  584.7   9.0   6.8e-180  584.6   9.0    1.0  1  lcl|NCBI__GCF_000016505.1:WP_012103792.1  CKL_RS16885 Asp-tRNA(Asn)/Glu-tR


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016505.1:WP_012103792.1  CKL_RS16885 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.6   9.0  6.8e-180  6.8e-180       2     480 ..       1     473 [.       1     474 [. 0.98

  Alignments for each domain:
  == domain 1  score: 584.6 bits;  conditional E-value: 6.8e-180
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e+viGlEvHv l t++K++c cs+ + + +pN++vcpvclglPG+lP lNk++v+ A+k +laln+
  lcl|NCBI__GCF_000016505.1:WP_012103792.1   1 MEFEAVIGLEVHVELLTETKIYCGCSTAFGS-EPNKHVCPVCLGLPGSLPRLNKKVVEYAIKAGLALNC 68 
                                               689****************************.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                                i+ ++s  dRK+YfY D Pk+yqitqq++Pi+++G +ei  + +e k+igier+h+EeD+gk+ ++  
  lcl|NCBI__GCF_000016505.1:WP_012103792.1  69 SIN-NKSRMDRKNYFYADCPKNYQITQQEIPICREGFIEIRNHLGEkKRIGIERIHMEEDAGKLIHTD- 135
                                               *65.7***********************************998766499*****************94. PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                  + +l+D+NR+g+PL+EiV+kPd++++kea+ +l++lr+il+++++sd+++e+Gs+R+D+N+sir+k
  lcl|NCBI__GCF_000016505.1:WP_012103792.1 136 ---EGTLIDYNRAGIPLIEIVSKPDIRTSKEAVSYLEDLRNILKFIGVSDCKMEQGSLRCDCNISIRPK 201
                                               ...469*************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRY 276
                                                + k g + EiKN+ns+k++ekai+yE++Rq++l+++ge+v qetr ++++k++t  +R+Ke ++DYRY
  lcl|NCBI__GCF_000016505.1:WP_012103792.1 202 HNLKLGVKTEIKNMNSFKALEKAIQYEYKRQSDLIESGEKVRQETRRWNDAKNVTEVMRSKEYANDYRY 270
                                               ********************************************************************* PP

                                 TIGR00133 277 fpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikep 345
                                               fpe dl+ i+i+++++++ +++++pelP++k  r+++e+++s ++ ++l+ ++e+ d fe+++kl+++p
  lcl|NCBI__GCF_000016505.1:WP_012103792.1 271 FPEGDLTAINISDNYIDN-IRKTIPELPDKKIDRFVEEFKISRKEIEILILNMEIGDFFENAAKLSGDP 338
                                               ******************.************************************************** PP

                                 TIGR00133 346 klavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliek 414
                                               k + nWi+ ++ +  +++ i+l++ +++  +laeli++i+ g+is+ ++k+++ee++ ++k+p+++i++
  lcl|NCBI__GCF_000016505.1:WP_012103792.1 339 KSVSNWITGDISRLAKETGIPLNNLNFTERDLAELIEFINCGVISNNIGKKVIEEMFYKGKSPRQIIHE 407
                                               ********************************************************************* PP

                                 TIGR00133 415 lgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               +g +q s ++++ k+v+ev++enpk++e+yk+gk+ka+kf++G vmkktkg a+p  v+kl++e +
  lcl|NCBI__GCF_000016505.1:WP_012103792.1 408 KGFVQNSSKEKILKVVKEVMEENPKSIEDYKKGKKKAVKFMIGMVMKKTKGNANPMLVNKLVEEEI 473
                                               ***************************************************************976 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.77
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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