Alignments for a candidate for gabT in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Shewanella loihica PV-4

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 5210744 Shew_3172 4-aminobutyrate aminotransferase (RefSeq)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__PV4:5210744
          Length = 426

 Score =  463 bits (1191), Expect = e-135
 Identities = 230/421 (54%), Positives = 294/421 (69%), Gaps = 1/421 (0%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           SN EL  R+ QAI RG G  +P++ +RA N  +WDVEG+ Y+DF  GIAV NTGH HPKV
Sbjct: 2   SNAELQARKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKV 61

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           VAAV+AQL   SHTC  V  YE  + L E +N+  PG   KK + VTTG+EAVEN VKIA
Sbjct: 62  VAAVKAQLDNFSHTCVMVNPYESAVALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIA 121

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RA T R G IAF+G +HGRT+ T+ALTGK+ PY    G   G ++ A YP   HG+S  D
Sbjct: 122 RAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGDIFHAPYPVAFHGVSVKD 181

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           ++ +I  +FK D AP D+AAIV+EPVQGEGGFYA+ P F+Q LRALCD+HGI+L+ DE+Q
Sbjct: 182 SLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLVMDEIQ 241

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           +G GRTG +F+ E  GV PDL T AK IAGGFPLA V G++E+MDA  PGGLGGTY G+P
Sbjct: 242 TGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSP 301

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFE 361
           + CVAAL VL+V ++E L+++A  +G      L A+ E++P+ IG+VR  GAMIA+EL  
Sbjct: 302 VGCVAALAVLEVMQEEQLVERAVKIGDSFNQALSALKEQYPQLIGEVRNQGAMIAMELVI 361

Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCF 421
           DGD  +P+  LT  I+A A   GL+LL+CG Y NV+R L  LTI D  + +GL      F
Sbjct: 362 DGDIEQPNTALTQAIIANAAAHGLVLLACGFYGNVIRFLPALTISDEIMAEGLAKFKTLF 421

Query: 422 D 422
           +
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: 566
Number of extensions: 19
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: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 5210744 Shew_3172 (4-aminobutyrate aminotransferase (RefSeq))
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.27153.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
     1e-178  580.2   5.4   1.3e-178  579.9   5.4    1.0  1  lcl|FitnessBrowser__PV4:5210744  Shew_3172 4-aminobutyrate aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210744  Shew_3172 4-aminobutyrate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.9   5.4  1.3e-178  1.3e-178       2     413 ..       9     416 ..       8     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 579.9 bits;  conditional E-value: 1.3e-178
                        TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 
                                      r+ +a+++G g++ +v++ +a +ael dv+G+r+id+++giav n+GhshPkvv+avk q++++ ht+ +v pyes v
  lcl|FitnessBrowser__PV4:5210744   9 RKVQAIARGQGNAYPVYVERALNAELWDVEGKRYIDFGTGIAVCNTGHSHPKVVAAVKAQLDNFSHTCVMVNPYESAV 86 
                                      7899************************************************************************** PP

                        TIGR00700  80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfape 157
                                      +lae+ln+iaPg  +kka+++++Gaeaven vkiar++tgr+gv+af++gfhGrtnltmalt+k++Pyk  fGPfa++
  lcl|FitnessBrowser__PV4:5210744  87 ALAEQLNRIAPGGSDKKAIFVTTGAEAVENCVKIARAHTGRRGVIAFNGGFHGRTNLTMALTGKITPYKHQFGPFAGD 164
                                      ****************************************************************************** PP

                        TIGR00700 158 vyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivli 235
                                      +++aP+p  +++ ++      +d l+aie+lf++d+++ +vaa+v+ePvqGeGGf  ++ e+++a++ lc++hgivl+
  lcl|FitnessBrowser__PV4:5210744 165 IFHAPYPVAFHGVSV------KDSLKAIEHLFKVDIAPCDVAAIVVEPVQGEGGFYAAPPEFLQALRALCDQHGIVLV 236
                                      ***********9988......44667**************************************************** PP

                        TIGR00700 236 adevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldii 313
                                       de+qtGf rtGk+f++eh +++Pdl+t+ak++a+G+Pl++vvG++ei+dap pGglGGty+G+P+++ aalavl+++
  lcl|FitnessBrowser__PV4:5210744 237 MDEIQTGFGRTGKMFSCEHAGVEPDLMTMAKGIAGGFPLAAVVGKSEIMDAPLPGGLGGTYGGSPVGCVAALAVLEVM 314
                                      ****************************************************************************** PP

                        TIGR00700 314 eeeglieraeqigklvkdklielkeevpa.igdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGi 389
                                      +ee l+era +ig   ++ l  lke+ p+ ig+vr++Gamia+elv d d ++P++al+++i a+a a+Gl+ll++G 
  lcl|FitnessBrowser__PV4:5210744 315 QEEQLVERAVKIGDSFNQALSALKEQYPQlIGEVRNQGAMIAMELViDGDIEQPNTALTQAIIANAAAHGLVLLACGF 392
                                      *************************998549***************9******************************* PP

                        TIGR00700 390 fGniirlltPltisdelldeglki 413
                                      +Gn+ir+l+ ltisde++ egl  
  lcl|FitnessBrowser__PV4:5210744 393 YGNVIRFLPALTISDEIMAEGLAK 416
                                      *********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (426 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: 10.53
//
[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, or view the source code.

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