Alignments for a candidate for gabT in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Burkholderia phytofirmans PsJN

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__BFirm:BPHYT_RS22435
          Length = 427

 Score =  602 bits (1552), Expect = e-177
 Identities = 294/421 (69%), Positives = 342/421 (81%)

Query: 3   MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62
           MKN EL  R+  ATPRGVGVMCDFYA+RAENA LWDVEGR + DFAAGIAV NTGHRHP+
Sbjct: 1   MKNAELKSRKDAATPRGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPK 60

Query: 63  VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122
           ++ AI  QL+ FTHTAYQIVPY  YV LAE++N   P     KTA FTTGAEAVENAIKI
Sbjct: 61  ILAAIRDQLDHFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKI 120

Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182
           ARA TGRPGVIAF+G FHGRTL+GMALTGKVAPYKIGFGPFPSD++HAPFP+ LHGV+T 
Sbjct: 121 ARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTA 180

Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242
            +L+A+E LFK DIDP RVAAII EPVQGEGGF  APA+F+R LR +C++HGI+LIADEV
Sbjct: 181 DSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEV 240

Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302
           QTGF RTGK+FAM H+DV PDL+T+AKSLAGGMPLS V GRA +MDA  PGGLGGTYAGN
Sbjct: 241 QTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGN 300

Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362
           PLAVAAAHAV+D+I+EEKLCER+  LG +++  L+A +   P +A+VRG G MVA EFC 
Sbjct: 301 PLAVAAAHAVLDIIDEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCK 360

Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
               +P AE  KRVQTRALE GL+LL CG Y NV+RFL+PLTI  A FD A+A+L   + 
Sbjct: 361 AGGTEPDAEFTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIK 420

Query: 423 E 423
           +
Sbjct: 421 D 421


Lambda     K      H
   0.321    0.136    0.400 

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: 645
Number of extensions: 17
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: 423
Length of database: 427
Length adjustment: 32
Effective length of query: 391
Effective length of database: 395
Effective search space:   154445
Effective search space used:   154445
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate BPHYT_RS22435 BPHYT_RS22435 (4-aminobutyrate aminotransferase)
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.21629.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.6e-199  648.7   1.0   1.8e-199  648.5   1.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS22435  BPHYT_RS22435 4-aminobutyrate am


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS22435  BPHYT_RS22435 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.5   1.0  1.8e-199  1.8e-199       2     420 .]       9     421 ..       8     421 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.5 bits;  conditional E-value: 1.8e-199
                                TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafq 71 
                                              r++aa+++Gvgv+++++a +ae+ael dv+G+r+id+aagiav n+Gh+hPk+++a++ q++++thta+q
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435   9 RKDAATPRGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQ 78 
                                              899******************************************************************* PP

                                TIGR00700  72 vvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmalt 141
                                              +vpy syvelaekln+ aPg ++kk++++++Gaeavena+kiar+ tgrpgv+af++gfhGrt + malt
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435  79 IVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMALT 148
                                              ********************************************************************** PP

                                TIGR00700 142 akvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGG 211
                                              +kv+PykiGfGPf+++v++aP+p ++++ ++       d l+aie lf+ad+++++vaa+++ePvqGeGG
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435 149 GKVAPYKIGFGPFPSDVFHAPFPNPLHGVTT------ADSLKAIEFLFKADIDPKRVAAIIFEPVQGEGG 212
                                              ****************************998......34677**************************** PP

                                TIGR00700 212 fivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGra 281
                                              f  ++ e+v a+++lc+ehgi+liadevqtGfartGklfa++h+d++Pdl+tvaksla+G+Plsgv+Gra
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435 213 FYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRA 282
                                              ********************************************************************** PP

                                TIGR00700 282 eildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGa 351
                                              +++da+apGglGGtyaGnPlavaaa+avldii+ee l+era  +g +vk kli l+  vp+i+dvrg G 
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435 283 DVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIIDEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGG 352
                                              ********************************************************************** PP

                                TIGR00700 352 miavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaalad 420
                                              m+ave+ +++ tePda  +++++++al++Gllll +G++ n++r+l Plti d+ +de++ ile++++d
  lcl|FitnessBrowser__BFirm:BPHYT_RS22435 353 MVAVEFCKAGGTEPDAEFTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIKD 421
                                              *****************************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (427 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.57
//
[ok]

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

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Protein sequences (fasta format)
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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