Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate Pf6N2E2_4013 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 Length = 425 Score = 815 bits (2106), Expect = 0.0 Identities = 413/425 (97%), Positives = 418/425 (98%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MSKTNA LM RR AAVPRGVGQIHPIFA+SAKNATVTDVEGREFIDFAGGIAVLNTGHVH Sbjct: 1 MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV Sbjct: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD Sbjct: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLV GLKAIQ KYPVIG+VRALGAMIAVEL Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVEL 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLT+PD QLDKGLAI+EE Sbjct: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEE 420 Query: 421 CFAEL 425 CF+EL Sbjct: 421 CFSEL 425 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: 814 Number of extensions: 21 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 Pf6N2E2_4013 (5-aminovalerate aminotransferase (EC 2.6.1.48) / 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.11739.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-167 542.3 7.3 3.7e-167 542.1 7.3 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 5-aminovalerate aminotransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:a # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 542.1 7.3 3.7e-167 3.7e-167 2 418 .. 11 422 .. 10 424 .. 0.99 Alignments for each domain: == domain 1 score: 542.1 bits; conditional E-value: 3.7e-167 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveel 65 rr+aav++Gvg +++a +a++a++ dv+G+++id+a+giavln+Gh hPk+++av +q+++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 11 RRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKL 74 89************************************************************** PP TIGR00700 66 thtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrg 129 tht+fqv+ ye yvel ek+na Pg kk++l+++G+eavenavkiar+ tgr gv+af+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 75 THTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGA 138 **************************************************************** PP TIGR00700 130 fhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadv 193 +hGrt +t+ lt+kv Py G+G +++ ++ra +p ++++ + dd +a+ie++f+ d lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSI------DDSIASIERIFKNDA 196 ***************************************9877......88899********** PP TIGR00700 194 eaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaiehedd 257 e++++aa+++ePvqGeGGf v++ke+++ ++ lc++hgi+liadevqtG rtG++fa+e +++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 197 EPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQMGV 260 **************************************************************** PP TIGR00700 258 kPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglier 321 dl t aks+a+G+Pl+gv G+ae +da apGglGGtyaG+P+a+aaalav+++ eee l +r lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 261 AADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDR 324 **************************************************************** PP TIGR00700 322 aeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlll 384 ++ +g+++ l ++++ p+igdvr lGamiavel + d+++P+aa +++ a+a+ +Gl+l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 325 CKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELFeNGDSHKPNAAAVAQVVAKARDKGLIL 388 ***********************************9968899********************** PP TIGR00700 385 ltaGifGniirlltPltisdelldeglkileaal 418 l++G +Gn++r+l Plt +de+ld+gl ile+ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4013 389 LSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECF 422 ******************************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: 00:00:00.02 # Mc/sec: 7.64 // [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