Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate 15422 b1302 GABA aminotransferase, PLP-dependent (NCBI)
Query= SwissProt::P50457 (421 letters) >FitnessBrowser__Keio:15422 Length = 421 Score = 832 bits (2148), Expect = 0.0 Identities = 421/421 (100%), Positives = 421/421 (100%) Query: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD Sbjct: 1 MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60 Query: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI Sbjct: 61 LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120 Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ Sbjct: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180 Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV Sbjct: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240 Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN Sbjct: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300 Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND Sbjct: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360 Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS Sbjct: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDALS 420 Query: 421 D 421 D Sbjct: 421 D 421 Lambda K H 0.319 0.134 0.388 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: 841 Number of extensions: 20 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: 421 Length of database: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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: 50 (23.9 bits)
Align candidate 15422 b1302 (GABA aminotransferase, PLP-dependent (NCBI))
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.16522.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-233 760.9 4.2 1.6e-233 760.7 4.2 1.0 1 lcl|FitnessBrowser__Keio:15422 b1302 GABA aminotransferase, PLP Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:15422 b1302 GABA aminotransferase, PLP-dependent (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 760.7 4.2 1.6e-233 1.6e-233 1 420 [] 8 421 .] 8 421 .] 1.00 Alignments for each domain: == domain 1 score: 760.7 bits; conditional E-value: 1.6e-233 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpyesyv 79 qrr++a+++Gvgv+++++a++ae+a+lkdv+Gn++id+aagiavln+Gh+hP++v+av++q++++thta+q+vpyesyv lcl|FitnessBrowser__Keio:15422 8 QRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYV 86 89***************************************************************************** PP TIGR00700 80 elaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapev 158 +laek+na+aP+sg++k++++++Gaeavenavkiar++tgrpgv+afs+gfhGrt++tmalt+kv+PykiGfGPf+++v lcl|FitnessBrowser__Keio:15422 87 TLAEKINALAPVSGQAKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSV 165 ******************************************************************************* PP TIGR00700 159 yraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliad 237 y++P+p+d+++i++ q+sld aie+lf++d+ea+qvaa+++ePvqGeGGf+v++kelvaa+++lc+ehgiv+iad lcl|FitnessBrowser__Keio:15422 166 YHVPYPSDLHGIST--QDSLD----AIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIAD 238 *************9..99999....****************************************************** PP TIGR00700 238 evqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316 evq+GfartGklfa++h++dkPdl+t+aksla+G+PlsgvvG+a+i+dapapGglGGtyaGnPlavaaa+avl+ii++e lcl|FitnessBrowser__Keio:15422 239 EVQSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKE 317 ******************************************************************************* PP TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniir 395 +l+era+q+g+++k++li++ke+vpai++vrglG+miave++dp+t+eP+aa+a+ki+++ala+Gllllt+G++Gn+ir lcl|FitnessBrowser__Keio:15422 318 SLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFNDPQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIR 396 ******************************************************************************* PP TIGR00700 396 lltPltisdelldeglkileaalad 420 +l+Plti+d+++d+++kil++al+d lcl|FitnessBrowser__Keio:15422 397 FLYPLTIPDAQFDAAMKILQDALSD 421 ***********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (421 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: 9.51 // [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