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.14985.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.02
//
[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:

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