Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2E2

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373
          Length = 430

 Score =  436 bits (1121), Expect = e-127
 Identities = 220/416 (52%), Positives = 288/416 (69%), Gaps = 1/416 (0%)

Query: 8   LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67
           L ++R    PRG+        DRA+ + LWDV+G+ Y DF  GI VLN GH HP+V+ A+
Sbjct: 11  LLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAV 70

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL++ +H  +Q+V Y+ Y+ LA+R+  ++  Q   K A FT+GAEAVENA+KIARAHT
Sbjct: 71  QAQLQKISHACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHT 130

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
            R  VIAF G FHGRTLLG  LTG   PYK  FGPF  +++H P+P+A  GV++  ALQA
Sbjct: 131 NRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSAMALQA 190

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L+ L  T + P RVAAII+EPVQG+GGF +APA+F++GLRA+  +HGIVLI DE+QTGFG
Sbjct: 191 LDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFG 250

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK F   H  ++PDL+T+AKSLAGG+PLS V G+A IMDAPLPGGLGGTY GN L+ A
Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCA 310

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQ 367
           AA AVI+  E+E+L  R   LG++LR+ LL  +   P + +VRG G M+A E       +
Sbjct: 311 AALAVIEAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIKHDEAR 370

Query: 368 -PSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
            P A+  +R+   A   GL+++ CG Y NV+RFL PL   +AQ D AL +L  ALA
Sbjct: 371 TPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQILDGALA 426


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: 549
Number of extensions: 22
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: 423
Length of database: 430
Length adjustment: 32
Effective length of query: 391
Effective length of database: 398
Effective search space:   155618
Effective search space used:   155618
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 Pf6N2E2_373 (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.32556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   7.6e-164  531.2   0.2   8.6e-164  531.0   0.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373  Gamma-aminobutyrate:alpha-ketogl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373  Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  531.0   0.2  8.6e-164  8.6e-164       2     419 ..      14     426 ..      13     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 531.0 bits;  conditional E-value: 8.6e-164
                                     TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelt 66 
                                                   +r+++v++G+ ++ + ++ +a+g+el dvdG+r++d+ +gi+vln+Gh+hPkvv+av+ q++++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373  14 QRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKIS 78 
                                                   79*************************************************************** PP

                                     TIGR00700  67 htafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfh 131
                                                   h++fqvv y+ y++la++l+++  g +  ka++++sGaeavenavkiar++t+r +v+af +gfh
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373  79 HACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGGFH 143
                                                   ***************************************************************** PP

                                     TIGR00700 132 GrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveae 196
                                                   Grt l  +lt+ ++Pyk  fGPfapev+++P+p  yr+ ++    ++   l+a+++l  ++v++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 144 GRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTS----AMA--LQALDELLATQVAPE 202
                                                   *************************************9987....444..88************* PP

                                     TIGR00700 197 qvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdl 261
                                                   +vaa+++ePvqG+GGf  ++ e+++ ++ l ++hgivli de+qtGf rtGk f  +h + +Pdl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 203 RVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLILDEIQTGFGRTGKWFGFQHAGIQPDL 267
                                                   ***************************************************************** PP

                                     TIGR00700 262 itvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqig 326
                                                   +tvaksla+GlPlsgvvG+aei+dap pGglGGty+Gn l++aaalav++  e+e l  r e +g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 268 VTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLARGEVLG 332
                                                   ***************************************************************** PP

                                     TIGR00700 327 klvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGif 390
                                                   +++++ l++l+   p+igdvrg G m+a+el+ + +++ Pda l +++  +a+a Gll++ +G++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 333 ERLRQGLLHLQTRYPQIGDVRGSGFMLAIELIkHDEARTPDADLNQRLIDEARAGGLLVIKCGVY 397
                                                   *******************************9566799*************************** PP

                                     TIGR00700 391 GniirlltPltisdelldeglkileaala 419
                                                    n++r+l+Pl+ s++++de+l+il  ala
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 398 RNVLRFLAPLVTSEAQIDEALQILDGALA 426
                                                   ************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (430 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.52
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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