Alignments for a candidate for gabT in Desulfacinum infernum DSM 9756

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Desulfacinum infernum DSM 9756

Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_073036559.1 BUB04_RS02225 4-aminobutyrate--2-oxoglutarate transaminase

Query= curated2:P94427
         (436 letters)



>NCBI__GCF_900129305.1:WP_073036559.1
          Length = 436

 Score =  427 bits (1097), Expect = e-124
 Identities = 209/421 (49%), Positives = 284/421 (67%)

Query: 16  KRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQ 75
           +R + V+   ++       +G GA LYD++GR +IDFAG I  +NVGHSHPKVV A++ Q
Sbjct: 13  RRSRVVTSAYASLRPCYIERGAGARLYDVEGREYIDFAGGIAVMNVGHSHPKVVAAIQEQ 72

Query: 76  AEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKIARKYTKRQ 135
           A++L H  F V+ Y   + LAEKL    PG   K A+F+NSGAEAVENAVK+AR ++KRQ
Sbjct: 73  AQKLTHTCFMVLPYEPAVLLAEKLAQAVPGRFPKSAVFVNSGAEAVENAVKVARYHSKRQ 132

Query: 136 GVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDM 195
            V++F   FHGRT +TMS+TSK+KPYK GFGPFAPEVY+ PF Y Y+ P  +     +  
Sbjct: 133 AVIAFENAFHGRTLLTMSLTSKIKPYKLGFGPFAPEVYRMPFAYCYRCPFQLRYPQCETA 192

Query: 196 VIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQ 255
              +  +FF+  VA E  A +++EP+QGEGGFI P   +   + + C+E G++F+ADEIQ
Sbjct: 193 CADSLREFFLTHVAAENTAALIVEPIQGEGGFITPPPEYFPKLKAICEEFGVLFIADEIQ 252

Query: 256 TGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLDAAAPGELGGTYAGSP 315
           TG  RTGT FA+EH++V  D+ TV+KSLAAG+PL  V+G+ E++D+  PG LGGTY G+P
Sbjct: 253 TGMGRTGTLFAMEHWNVEADITTVAKSLAAGMPLGAVVGKKEIMDSVHPGGLGGTYGGNP 312

Query: 316 LGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKD 375
           + CAAALAV D+IE E L +R+  +G+ +  +  E    F  IG++R LG M A+E+VKD
Sbjct: 313 VACAAALAVFDVIETEDLLDRARRLGEKLRRRLDEMHGRFQCIGEVRGLGPMLALELVKD 372

Query: 376 PDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISDSLLNEGLSILEAGLR 435
            +T+EP    A  +  Y    GL+LL+ G  GN+IR L PLVI D LL+ GL ILE G  
Sbjct: 373 RETKEPAPDAAKRLTDYCFDRGLVLLSCGTFGNVIRLLMPLVIEDELLDRGLQILEEGFL 432

Query: 436 A 436
           A
Sbjct: 433 A 433


Lambda     K      H
   0.319    0.136    0.393 

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: 475
Number of extensions: 11
Number of successful extensions: 1
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_073036559.1 BUB04_RS02225 (4-aminobutyrate--2-oxoglutarate transaminase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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.carbon/TIGR00700.hmm
# target sequence database:        /tmp/gapView.2132678.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-174  564.8   0.0   5.7e-174  564.5   0.0    1.0  1  NCBI__GCF_900129305.1:WP_073036559.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129305.1:WP_073036559.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.5   0.0  5.7e-174  5.7e-174       2     417 ..      13     430 ..      12     433 .. 0.98

  Alignments for each domain:
  == domain 1  score: 564.5 bits;  conditional E-value: 5.7e-174
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr  +v++  +   + ++ ++ ga l+dv+G+++id+a+giav+nvGhshPkvv+a+++q+++ltht+f+v+p
  NCBI__GCF_900129305.1:WP_073036559.1  13 RRSRVVTSAYASLRPCYIERGAGARLYDVEGREYIDFAGGIAVMNVGHSHPKVVAAIQEQAQKLTHTCFMVLP 85 
                                           8999999999999************************************************************ PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye  v laekl++  Pg  +k av++nsGaeavenavk+ar +++r++v+af+++fhGrt ltm+lt+k+kPy
  NCBI__GCF_900129305.1:WP_073036559.1  86 YEPAVLLAEKLAQAVPGRFPKSAVFVNSGAEAVENAVKVARYHSKRQAVIAFENAFHGRTLLTMSLTSKIKPY 158
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqesldd.elaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219
                                           k+GfGPfapevyr+P++y yr + + +    +    ++++++f + v+ae+ aa+++eP+qGeGGfi p+ e+
  NCBI__GCF_900129305.1:WP_073036559.1 159 KLGFGPFAPEVYRMPFAYCYRCPFQLRYPQCETaCADSLREFFLTHVAAENTAALIVEPIQGEGGFITPPPEY 231
                                           **********************9988877776647789*********************************** PP

                             TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292
                                            ++++ +c+e g+++iade+qtG+ rtG+lfa+eh++++ d+ tvaksla+G+Pl +vvG+ ei+d+ +pGgl
  NCBI__GCF_900129305.1:WP_073036559.1 232 FPKLKAICEEFGVLFIADEIQTGMGRTGTLFAMEHWNVEADITTVAKSLAAGMPLGAVVGKKEIMDSVHPGGL 304
                                           ************************************************************************* PP

                             TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdtte 364
                                           GGty+GnP+a+aaalav+d+ie e l +ra+++g+ ++ +l e++  ++ ig+vrglG m+a+elv d +t+e
  NCBI__GCF_900129305.1:WP_073036559.1 305 GGTYGGNPVACAAALAVFDVIETEDLLDRARRLGEKLRRRLDEMHGRFQCIGEVRGLGPMLALELVkDRETKE 377
                                           ******************************************************************999**** PP

                             TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaa 417
                                           P    a++++ +   +Gl+ll++G fGn+irll+Pl+i delld gl+ile++
  NCBI__GCF_900129305.1:WP_073036559.1 378 PAPDAAKRLTDYCFDRGLVLLSCGTFGNVIRLLMPLVIEDELLDRGLQILEEG 430
                                           **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (436 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: 15.64
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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 2024 update 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

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 catabolism of small carbon sources