Alignments for a candidate for gabT in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Acidovorax sp. GW101-3H11

Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= metacyc::MONOMER-11537
         (425 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  555 bits (1430), Expect = e-162
 Identities = 276/417 (66%), Positives = 332/417 (79%)

Query: 4   TNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKI 63
           TNA+L+ RR AAV RGVGQ H +F   A+NA + DVEGR FIDFAGGIAVLNTGH+H  +
Sbjct: 33  TNAALLTRRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGV 92

Query: 64  IAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA 123
           IAAV  QL+  THTCFQV+AYEPYVE+CE++N   PG FAKK+LL+TTG+EAVENA+KIA
Sbjct: 93  IAAVKAQLDLYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIA 152

Query: 124 RAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDD 183
           RA T R GVIAFTG YHGRT +TLGLTGKV PY  G G  PG  + AL+PN LHGVS++ 
Sbjct: 153 RAYTKRPGVIAFTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQ 212

Query: 184 SIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQ 243
           ++ S+E IFKND EP  +AA I+EPVQGEGGFYVAP EF+  L+ L D++GILLIADEVQ
Sbjct: 213 ALHSVELIFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQ 272

Query: 244 TGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303
           TGAGRTGT+FA EQ  V  DL T AKS+AGGFPLAGV G+A+ MDA APGGLGGTYAGSP
Sbjct: 273 TGAGRTGTWFASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSP 332

Query: 304 IACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFEN 363
           +ACAA+LAV+E F +E LL R + +G  LV  LK + A+ P IG+VR LGAM+A+ELFEN
Sbjct: 333 VACAASLAVIEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFEN 392

Query: 364 GDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420
           GD  +P+AA   QVVA+A  +GLILLSCGT+GNV+R+LVPLT+ D  L +GLAI+ +
Sbjct: 393 GDLSRPDAALTKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILAD 449


Lambda     K      H
   0.320    0.137    0.394 

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: 636
Number of extensions: 21
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: 425
Length of database: 459
Length adjustment: 32
Effective length of query: 393
Effective length of database: 427
Effective search space:   167811
Effective search space used:   167811
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 Ac3H11_4179 (Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19))
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.10795.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.7e-174  564.1   1.2   8.9e-174  563.9   1.2    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179  Gamma-aminobutyrate:alpha-ketogl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179  Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.9   1.2  8.9e-174  8.9e-174       2     419 ..      40     452 ..      39     453 .. 0.98

  Alignments for each domain:
  == domain 1  score: 563.9 bits;  conditional E-value: 8.9e-174
                                        TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqve 63 
                                                      rr+aav++Gvg + + +++ka +ael dv+G+r+id+a+giavln+Gh h  v++avk q++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179  40 RRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGVIAAVKAQLD 101
                                                      8************************************************************* PP

                                        TIGR00700  64 elthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvva 125
                                                       +tht+fqvv ye yve+ e+ln++aPg+  kk++ll++Gaeavena+kiar+yt+rpgv+a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 102 LYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIARAYTKRPGVIA 163
                                                      ************************************************************** PP

                                        TIGR00700 126 fsrgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiea 187
                                                      f++g+hGrtnlt+ lt+kv+PykiGfGPf++e y+a +p  +++ ++  ++     l+++e 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 164 FTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSV--EQ----ALHSVEL 219
                                                      *******************************************9988..44....55699** PP

                                        TIGR00700 188 lfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGkl 249
                                                      +f+ d+e+e+vaa ++ePvqGeGGf v++ e+++ +++l ++ gi+liadevqtG  rtG+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 220 IFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQTGAGRTGTW 281
                                                      ************************************************************** PP

                                        TIGR00700 250 faieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavld 311
                                                      fa e + + Pdlit+aksla+G+Pl+gvvGra+++dapapGglGGtyaG+P+a+aa+lav++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 282 FASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSPVACAASLAVIE 343
                                                      ************************************************************** PP

                                        TIGR00700 312 iieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaek 372
                                                         +e l  r++++g l+   l +l + +paigdvrglGam+a+el  + d + Pdaal+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 344 AFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFeNGDLSRPDAALTKQ 405
                                                      *********************************************9968899********** PP

                                        TIGR00700 373 iaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419
                                                      + a+a  +Gl+ll++G +Gn+ir+l Plt sdell+egl il ++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4179 406 VVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSLE 452
                                                      *******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (459 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.86
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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