Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate PP_0214 PP_0214 4-aminobutyrate aminotransferase
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__Putida:PP_0214 Length = 425 Score = 738 bits (1905), Expect = 0.0 Identities = 370/425 (87%), Positives = 396/425 (93%), Gaps = 1/425 (0%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MSKTN SLM+RR AAVPRGVGQIHPIF D+AKN+TV DVEGRE IDFAGGIAVLNTGH+H Sbjct: 1 MSKTNESLMQRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PK++AAV EQL K++HTCFQVLAYEPYVELCEKIN VPGDF KKTLLVTTGSEAVENAV Sbjct: 61 PKVVAAVQEQLTKVSHTCFQVLAYEPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTG YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRAL+P+ELHG+S Sbjct: 121 KIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALFPSELHGIS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 +DD+IAS+ERIFKNDAEPRDIAAII+EPVQGEGGF APKE MKRLRALCDQHGILLIAD Sbjct: 181 VDDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRALCDQHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV DLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 GSPIACAAALAV+EVFEEE LLDR KAVGERL GL+ IQ KYP+IG+VR LG+MIAVE+ Sbjct: 301 GSPIACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEV 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 FE G +H PNAAAV QVVAKAR+KGLILLSCGTYGNVLR+LVPLT+ DA LDKGLAIIEE Sbjct: 361 FEKG-THTPNAAAVGQVVAKAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEE 419 Query: 421 CFAEL 425 CFAE+ Sbjct: 420 CFAEI 424 Lambda K H 0.320 0.137 0.394 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: 776 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: 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 PP_0214 PP_0214 (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.10294.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-169 548.3 4.9 5.3e-169 548.2 4.9 1.0 1 lcl|FitnessBrowser__Putida:PP_0214 PP_0214 4-aminobutyrate aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0214 PP_0214 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.2 4.9 5.3e-169 5.3e-169 1 418 [. 10 421 .. 10 423 .. 0.99 Alignments for each domain: == domain 1 score: 548.2 bits; conditional E-value: 5.3e-169 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvpy 75 qrr aav++Gvg ++++ a+++++ dv+G++lid+a+giavln+Gh hPkvv+av++q+ ++ ht+fqv+ y lcl|FitnessBrowser__Putida:PP_0214 10 QRRVAAVPRGVGQIHPIFVDTAKNSTVIDVEGRELIDFAGGIAVLNTGHLHPKVVAAVQEQLTKVSHTCFQVLAY 84 89************************************************************************* PP TIGR00700 76 esyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPykiG 150 e yvel ek+n++ Pg +kk++l+++G+eavenavkiar+ tgr gv+af++g+hGrt +t+ lt+kv Py G lcl|FitnessBrowser__Putida:PP_0214 85 EPYVELCEKINKLVPGDFDKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGGYHGRTMMTLGLTGKVVPYSAG 159 *************************************************************************** PP TIGR00700 151 fGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavas 225 +G +++ ++ra +p+++++i++ dd +a++e++f+ d e++++aa++lePvqGeGGf ++kel++ ++ lcl|FitnessBrowser__Putida:PP_0214 160 MGLMPGGIFRALFPSELHGISV------DDAIASVERIFKNDAEPRDIAAIILEPVQGEGGFLPAPKELMKRLRA 228 *******************988......88999****************************************** PP TIGR00700 226 lckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnP 300 lc++hgi+liadevqtG rtG++fa+e +++ Pdl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P lcl|FitnessBrowser__Putida:PP_0214 229 LCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAPDLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSP 303 *************************************************************************** PP TIGR00700 301 lavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdttePdaalaekiaa 375 +a+aaalav+++ eee l +r++ +g++++ l e++++ p igdvrglG+miave+ + +t+ P+aa ++ a lcl|FitnessBrowser__Putida:PP_0214 304 IACAAALAVIEVFEEEKLLDRSKAVGERLTAGLREIQKKYPIIGDVRGLGSMIAVEVFEKGTHTPNAAAVGQVVA 378 *************************************************************************** PP TIGR00700 376 aalaaGlllltaGifGniirlltPltisdelldeglkileaal 418 +a+++Gl+ll++G +Gn++r+l Plt d+lld+gl i+e+ + lcl|FitnessBrowser__Putida:PP_0214 379 KAREKGLILLSCGTYGNVLRILVPLTAEDALLDKGLAIIEECF 421 ***************************************9876 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: 11.36 // [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