Alignments for a candidate for gabT in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Escherichia coli BW25113

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 16752 b2662 4-aminobutyrate aminotransferase (NCBI)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Keio:16752
          Length = 426

 Score =  848 bits (2191), Expect = 0.0
 Identities = 426/426 (100%), Positives = 426/426 (100%)

Query: 1   MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60
           MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP
Sbjct: 1   MNSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHP 60

Query: 61  KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120
           KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK
Sbjct: 61  KVVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVK 120

Query: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180
           IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE
Sbjct: 121 IARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE 180

Query: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240
           DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE
Sbjct: 181 DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADE 240

Query: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300
           VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG
Sbjct: 241 VQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAG 300

Query: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF 360
           NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF
Sbjct: 301 NPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELF 360

Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC 420
           EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC
Sbjct: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC 420

Query: 421 FDEAKQ 426
           FDEAKQ
Sbjct: 421 FDEAKQ 426


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: 828
Number of extensions: 15
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: 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 16752 b2662 (4-aminobutyrate aminotransferase (NCBI))
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.11585.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-166  540.3   0.6   1.5e-166  540.1   0.6    1.0  1  lcl|FitnessBrowser__Keio:16752  b2662 4-aminobutyrate aminotrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16752  b2662 4-aminobutyrate aminotransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.1   0.6  1.5e-166  1.5e-166       1     417 [.       9     420 ..       9     423 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.1 bits;  conditional E-value: 1.5e-166
                       TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 
                                     qrr +a+++Gvg   +++a +ae++ + dv+G++++d+a+giavln+Gh hPkvv+av+ q+++l ht+fqv+ ye y+
  lcl|FitnessBrowser__Keio:16752   9 QRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYL 87 
                                     89***************************************************************************** PP

                       TIGR00700  80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapev 158
                                     el e +n+  Pg   kk++l+++G+eavenavkiar+ t+r g +afs+++hGrt+ t+alt+kv+Py  G+G ++++v
  lcl|FitnessBrowser__Keio:16752  88 ELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHV 166
                                     ******************************************************************************* PP

                       TIGR00700 159 yraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliad 237
                                     yra +p ++++i+       dd +a+i+++f+ d ++e++aa+v+ePvqGeGGf  ++  +++ ++ lc+ehgi+liad
  lcl|FitnessBrowser__Keio:16752 167 YRALYPCPLHGISE------DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIAD 239
                                     ***********988......78899****************************************************** PP

                       TIGR00700 238 evqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316
                                     evq+G  rtG+lfa+e +++ Pdl t aks+a+G+Pl+gv+Grae++da apGglGGtyaGnP+a+ aal vl++ e+e
  lcl|FitnessBrowser__Keio:16752 240 EVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQE 318
                                     ******************************************************************************* PP

                       TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGnii 394
                                      l ++a+++g+ +kd l+ + e+ p igdvrglGamia+el  d d ++Pda l+++i a+a+ +Gl+ll++G + n++
  lcl|FitnessBrowser__Keio:16752 319 NLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFeDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVL 397
                                     ****************************************998999********************************* PP

                       TIGR00700 395 rlltPltisdelldeglkileaa 417
                                     r+l Plti d+++ +gl+i+++ 
  lcl|FitnessBrowser__Keio:16752 398 RILVPLTIEDAQIRQGLEIISQC 420
                                     *******************9875 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.10
//
[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