Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N1B4

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910
          Length = 430

 Score =  435 bits (1118), Expect = e-126
 Identities = 219/416 (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  QAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHT 130

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

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L+ L  T + P RVAAII+EPVQG+GGF +AP +F++ LRA+  +HGIVLI DE+QTGFG
Sbjct: 191 LDELLATQVAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFG 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 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFC-DPATG 366
           AA AVI+  E+E+L  R  +LG++LRE LL  +   P + +VRG G M+A E   D    
Sbjct: 311 AALAVIEAYEQEQLLARGEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELIKDDDAR 370

Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422
            P A+  +R+   A   GL+++ CG Y NV+RFL PL   +AQ D AL +L  ALA
Sbjct: 371 TPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQILDAALA 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: 529
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: 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 Pf1N1B4_4910 (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.11087.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.7e-165  536.6   0.1     2e-165  536.4   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910  Gamma-aminobutyrate:alpha-ketogl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910  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 !  536.4   0.1    2e-165    2e-165       2     419 ..      14     426 ..      13     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 536.4 bits;  conditional E-value: 2e-165
                                      TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveel 65 
                                                    +r+++v++G+ ++ + ++ +a+g+el dvdG+r++d+ +gi+vln+Gh+hPkvv+av+ q++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910  14 QRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKV 77 
                                                    79************************************************************** PP

                                      TIGR00700  66 thtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrg 129
                                                     h++fqvv y+ y++la++l+++  g +  ka++++sGaeavenavkiar++t+r +v+af +g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910  78 SHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGG 141
                                                    **************************************************************** PP

                                      TIGR00700 130 fhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadv 193
                                                    fhGrt l  +lt+ ++Pyk  fGPfapev+++P+p  yr+ ++      d  l+a+++l  ++v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 142 FHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTS------DMALKALDELLATQV 199
                                                    ***************************************9987......44566********** PP

                                      TIGR00700 194 eaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaiehedd 257
                                                    ++e+vaa+++ePvqG+GGf  ++ e+++a++ l  +hgivli de+qtGf rtGk f  +h + 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 200 APERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFGRTGKWFGFQHAGI 263
                                                    **************************************************************** PP

                                      TIGR00700 258 kPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglier 321
                                                    +Pdl+tvaksla+GlPlsgvvG+aei+dap pGglGGty+Gn l++aaalav++  e+e l  r
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 264 QPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLAR 327
                                                    **************************************************************** PP

                                      TIGR00700 322 aeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlll 384
                                                     e +g+++++ l+ l++  p+igdvrg G m+a+el+ d d++ Pda l +++  +a+a Gll+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 328 GEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELIkDDDARTPDADLNQRLIDEARAGGLLV 391
                                                    ***********************************998999*********************** PP

                                      TIGR00700 385 ltaGifGniirlltPltisdelldeglkileaala 419
                                                    + +G++ n++r+l+Pl+ s++++de+l+il aala
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 392 IKCGVYRNVLRFLAPLVTSEAQVDEALQILDAALA 426
                                                    ********************************997 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.36
//
[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