GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Halomonas xinjiangensis TRM 0175

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_043527315.1 JH15_RS04225 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000759345.1:WP_043527315.1
          Length = 432

 Score =  419 bits (1076), Expect = e-121
 Identities = 206/421 (48%), Positives = 278/421 (66%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           +N +L + + + +  G       FADRAEN  +WD +G   +DFAGGI VLN GH HPKV
Sbjct: 2   NNAQLNELKQRYVANGAASPATQFADRAENALIWDADGNRLIDFAGGIGVLNIGHRHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           V AV+AQL K+ HTC  V+ YE Y+++ E ++Q  P     K +L  +G+EA+ENAVK+A
Sbjct: 62  VEAVKAQLDKVMHTCQTVMPYEGYVKVAEKLSQITPVRGHAKVMLANSGAEALENAVKVA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RAAT ++  I F G YHGRT  T+A+ GKV PY+   G MPG+V+RA YP P HG+SED+
Sbjct: 122 RAATGKNNVICFDGGYHGRTFMTMAMNGKVAPYATDFGSMPGNVFRAPYPVPYHGVSEDE 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+  +    K DA P+D AAIV+EPV GEGGFYA+  +F++ +R +CDEHGI+LI DEVQ
Sbjct: 182 ALRGLKMALKTDANPKDTAAIVLEPVLGEGGFYAAPASFLKAIRDICDEHGILLIIDEVQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           SG GRTG +FA+E  GV PD+   AKS+A G P++ V G  +VMDA     LGGTY G+P
Sbjct: 242 SGFGRTGKMFAIEHSGVEPDIICMAKSMADGMPISAVVGTDKVMDASGGNSLGGTYTGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
           ++C A L VL+VFE+E +L+K+  LG KL        +    + + R LGAM A +L  D
Sbjct: 302 VSCAATLAVLEVFEEEKILEKSQALGDKLAKRFSQWEQDFDCVDNGRNLGAMAAFDLVSD 361

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
              + PDA L   +  RAR+KGL+LLSCG Y N +R L+P+TIED  + +GL ++     
Sbjct: 362 KAQHTPDADLAGALCKRAREKGLVLLSCGLYGNTIRFLMPVTIEDDILEEGLGVVESALK 421

Query: 423 E 423
           E
Sbjct: 422 E 422


Lambda     K      H
   0.320    0.137    0.401 

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: 525
Number of extensions: 18
Number of successful extensions: 2
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: 426
Length of database: 432
Length adjustment: 32
Effective length of query: 394
Effective length of database: 400
Effective search space:   157600
Effective search space used:   157600
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_043527315.1 JH15_RS04225 (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.1690766.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-161  521.8   1.0     6e-161  521.6   1.0    1.0  1  NCBI__GCF_000759345.1:WP_043527315.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043527315.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.6   1.0    6e-161    6e-161       4     419 ..      11     421 ..       8     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 521.6 bits;  conditional E-value: 6e-161
                             TIGR00700   4 aaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpye 76 
                                           + +v++G +  ++ +a +ae+a + d dGnrlid+a+gi+vln+Gh+hPkvveavk q+++++ht+ +v+pye
  NCBI__GCF_000759345.1:WP_043527315.1  11 QRYVANGAASPATQFADRAENALIWDADGNRLIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTVMPYE 83 
                                           56799999999************************************************************** PP

                             TIGR00700  77 syvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPyki 149
                                           +yv++aekl++i+P+ g++k +l nsGaea+enavk+ar+ tg++ v++f++g+hGrt++tma+ +kv+Py +
  NCBI__GCF_000759345.1:WP_043527315.1  84 GYVKVAEKLSQITPVRGHAKVMLANSGAEALENAVKVARAATGKNNVICFDGGYHGRTFMTMAMNGKVAPYAT 156
                                           ************************************************************************* PP

                             TIGR00700 150 GfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaa 222
                                            fG ++++v+raP+p +y++ +   +e+    l+ ++   ++d ++++ aa+vlePv GeGGf  ++  +++a
  NCBI__GCF_000759345.1:WP_043527315.1 157 DFGSMPGNVFRAPYPVPYHGVSE--DEA----LRGLKMALKTDANPKDTAAIVLEPVLGEGGFYAAPASFLKA 223
                                           ********************988..555....5578888899******************************* PP

                             TIGR00700 223 vaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGt 295
                                           ++++c+ehgi+li devq+Gf rtGk+faieh +++Pd+i++aks+adG+P+s+vvG  +++da+    lGGt
  NCBI__GCF_000759345.1:WP_043527315.1 224 IRDICDEHGILLIIDEVQSGFGRTGKMFAIEHSGVEPDIICMAKSMADGMPISAVVGTDKVMDASGGNSLGGT 296
                                           ************************************************************************* PP

                             TIGR00700 296 yaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePda 367
                                           y+G+P+++aa+lavl++ eee + e+++ +g  + ++  ++++ ++ + + r+lGam+a +lv d   + Pda
  NCBI__GCF_000759345.1:WP_043527315.1 297 YTGSPVSCAATLAVLEVFEEEKILEKSQALGDKLAKRFSQWEQDFDCVDNGRNLGAMAAFDLVsDKAQHTPDA 369
                                           ***************************************************************8888899*** PP

                             TIGR00700 368 alaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                            la ++ ++a+++Gl+ll++G++Gn ir+l+P+ti d++l+egl ++e+al+
  NCBI__GCF_000759345.1:WP_043527315.1 370 DLAGALCKRAREKGLVLLSCGLYGNTIRFLMPVTIEDDILEEGLGVVESALK 421
                                           ************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (432 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: 00:00:00.00
# Mc/sec: 19.43
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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