Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file)
Query= uniprot:A1S8Y2 (425 letters) >FitnessBrowser__MR1:200454 Length = 425 Score = 735 bits (1898), Expect = 0.0 Identities = 367/423 (86%), Positives = 393/423 (92%) Query: 1 MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60 MS TNDSLM RR+AAVAGGVGQIHP+FT RAENA+VWDVEGRE+IDFAGGIAVLNTGHLH Sbjct: 1 MSTTNDSLMARRQAAVAGGVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLH 60 Query: 61 PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120 PKVKAAVA QLE FSHTCFMVLGYESY+ VCEKLNQLVPGDFAKK+ALFTSGSEAVENA+ Sbjct: 61 PKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAV 120 Query: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVS 180 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLM ANVFRAEFPCALHGVS Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVS 180 Query: 181 EDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIAD 240 +DDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYA +P FM+RLR LCDREGIMLIAD Sbjct: 181 DDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYG 300 EVQTGAGRTGTFFAMEQMGV+ADITTFAKSIAGGFPLSGITGRA+VMDAIGPGGLGGTYG Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYG 300 Query: 301 GSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360 G+PLACAAALAV+EVFEEEKLLER+NAIG IKSA+ + +PQIA+VRGLG+M AIEL Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIEL 360 Query: 361 MENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420 ME+GKPAP+YC Q+L EARNRGLILLSCGTYGNVLRILVP+T D Q+ GL I+ F Sbjct: 361 MEDGKPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVSDTQLDAGLGILKTSFN 420 Query: 421 AVL 423 AVL Sbjct: 421 AVL 423 Lambda K H 0.319 0.136 0.391 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: 647 Number of extensions: 6 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: 425 Length of database: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 200454 SO1276 (4-aminobutyrate aminotransferase (NCBI ptt file))
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.14883.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-163 530.5 5.3 1.4e-163 530.3 5.3 1.0 1 lcl|FitnessBrowser__MR1:200454 SO1276 4-aminobutyrate aminotran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200454 SO1276 4-aminobutyrate aminotransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 530.3 5.3 1.4e-163 1.4e-163 2 417 .. 11 418 .. 10 421 .. 0.98 Alignments for each domain: == domain 1 score: 530.3 bits; conditional E-value: 1.4e-163 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyve 80 rr+aav+ Gvg ++++a+ae+a + dv+G+++id+a+giavln+Gh hPkv +av q+e++ ht+f+v+ yesy++ lcl|FitnessBrowser__MR1:200454 11 RRQAAVAGGVGQIHPIFTARAENASVWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQ 89 89***************************************************************************** PP TIGR00700 81 laeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapevy 159 + ekln++ Pg kk++l++sG+eavenavk+ar+yt+r gv+af+ g+hGrt ++alt+kv+Py G+G ++++v+ lcl|FitnessBrowser__MR1:200454 90 VCEKLNQLVPGDFAKKTALFTSGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVF 168 ******************************************************************************* PP TIGR00700 160 raPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliade 238 ra +p +++ + dd +a+ie++f+ d e+ ++aa++lePvqGeGGf + +++ ++ lc+++gi+liade lcl|FitnessBrowser__MR1:200454 169 RAEFPCALHGVSD------DDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAVSPAFMQRLRALCDREGIMLIADE 241 *********9987......67788******************************************************* PP TIGR00700 239 vqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeg 317 vqtG rtG++fa+e +++ d+ t aks+a+G+Plsg++Gra+++da pGglGGty+GnPla+aaalavl++ eee lcl|FitnessBrowser__MR1:200454 242 VQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGRAQVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEK 320 ******************************************************************************* PP TIGR00700 318 lieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirl 396 l era+ ig ++k l +++ e p+i+dvrglGam a+el++ + +P +++i a+a+++Gl+ll++G +Gn++r+ lcl|FitnessBrowser__MR1:200454 321 LLERANAIGDRIKSALNTMQVEHPQIADVRGLGAMNAIELMEDG--KPAPQYCAQILAEARNRGLILLSCGTYGNVLRI 397 ****************************************9876..56666789999********************** PP TIGR00700 397 ltPltisdelldeglkileaa 417 l Plt+sd++ld+gl il+ + lcl|FitnessBrowser__MR1:200454 398 LVPLTVSDTQLDAGLGILKTS 418 ******************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (425 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: 10.15 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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