GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Pseudomonas fluorescens FW300-N2C3

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase

Query= BRENDA::Q0K2K2
         (423 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26715
          Length = 430

 Score =  434 bits (1117), Expect = e-126
 Identities = 220/415 (53%), Positives = 285/415 (68%), Gaps = 1/415 (0%)

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

Query: 68  AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127
            AQL++ +H  +Q+V Y+ Y+ L +R+  LV  Q   K ALFT+GAEAVENA+KIARAHT
Sbjct: 71  QAQLQKVSHACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHT 130

Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187
            RP VI+F G FHGRTLLG  LTG   PYK  FGPF  +++H P+P+A  G S+E ALQA
Sbjct: 131 NRPAVISFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQA 190

Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247
           L  L  T + P RVAAII+EPVQG+GGF +AP +F++ LR + +QHGIVLI DE+QTGFG
Sbjct: 191 LNELLATQVAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFG 250

Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307
           RTGK F   H  ++PDL+T+AKSLAGG+P+S V GRA IMDAPLPGGLGGTY GN L+ A
Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCA 310

Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFC-DPATG 366
           AA AVID  E+E+L ER   LG++LR+ LL  +   P + +VRG G M+A E   D    
Sbjct: 311 AALAVIDAYEQEQLLERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEAR 370

Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421
            P AE  +++  +A    L+++ CG + NV+RFL PL   ++Q D AL +L  AL
Sbjct: 371 SPDAELTQQLIDQARVGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425


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: 21
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 AO356_26715 AO356_26715 (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.8930.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.8e-162  526.0   0.0   3.2e-162  525.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715  AO356_26715 4-aminobutyrate amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715  AO356_26715 4-aminobutyrate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.8   0.0  3.2e-162  3.2e-162       2     418 ..      14     425 ..      13     427 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.8 bits;  conditional E-value: 3.2e-162
                                       TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqvee 64 
                                                     +r+++v++G+ ++ + ++ +a+gae+ dvdG r++d+ +gi+vln+Gh+hPkvv+av+ q+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715  14 QRDQFVPRGLVTAHPLVIDRAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQK 76 
                                                     79************************************************************* PP

                                       TIGR00700  65 lthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafs 127
                                                     + h++fqvv y+ y++l ++l+++  g +  ka+l++sGaeavenavkiar++t+rp+v++f 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715  77 VSHACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHTNRPAVISFR 139
                                                     *************************************************************** PP

                                       TIGR00700 128 rgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfv 190
                                                     +gfhGrt l  +lt+ ++Pyk  fGPfapev+++P+p  yr+ ++      +  l+a+++l  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 140 GGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSS------EMALQALNELLA 196
                                                     *****************************************9988......34578******* PP

                                       TIGR00700 191 adveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaie 253
                                                     ++v++++vaa+++ePvqG+GGf  ++ e+++a+++l ++hgivli de+qtGf rtGk f  +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 197 TQVAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGFQ 259
                                                     *************************************************************** PP

                                       TIGR00700 254 heddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316
                                                     h + +Pdl+tvaksla+GlP+sgvvGra+i+dap pGglGGty+Gn l++aaalav+d  e+e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 260 HAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDAYEQE 322
                                                     *************************************************************** PP

                                       TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaal 378
                                                      l er + +g+++++ l+ l++  p+igdvrg G m+a+el+ d +++ Pda l++++  +a+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 323 QLLERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIkDDEARSPDAELTQQLIDQAR 385
                                                     ****************************************9978999**************** PP

                                       TIGR00700 379 aaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                                        ll++ +G++ n++r+l+Pl+  ++++de+l ileaal
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 386 VGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425
                                                     *************************************998 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.46
//
[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:

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:

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:

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:

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