Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate PfGW456L13_494 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= metacyc::MONOMER-11537 (425 letters) >lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) Length = 425 Score = 819 bits (2116), Expect = 0.0 Identities = 414/425 (97%), Positives = 420/425 (98%) Query: 1 MSKTNASLMKRREAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MSKTNASLM RR AAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH Sbjct: 1 MSKTNASLMARRTAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PK+IAAVTEQLNKLTHTCFQVLAYEPYVE+CEKINAKVPGDFAKKTLLVTTGSEAVEN++ Sbjct: 61 PKVIAAVTEQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSI 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS Sbjct: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 IDDSIASIERIFKNDAEP+DIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD Sbjct: 181 IDDSIASIERIFKNDAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA Sbjct: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL Sbjct: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEE 420 FENGDSHKPNAAAVA VVAKARDKGLILLSCGTYGNVLRVLVPLTSPD QLDKGLAIIEE Sbjct: 361 FENGDSHKPNAAAVASVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE 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: 822 Number of extensions: 22 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 PfGW456L13_494 (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.30266.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-165 536.6 7.4 1.9e-165 536.4 7.4 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 5-aminovalerate aminotransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobu # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 536.4 7.4 1.9e-165 1.9e-165 2 418 .. 11 422 .. 10 424 .. 0.99 Alignments for each domain: == domain 1 score: 536.4 bits; conditional E-value: 1.9e-165 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvvea 57 rr+aav++Gvg +++a +a++a++ dv+G+++id+a+giavln+Gh hPkv++a lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 11 RRTAAVPRGVGQIHPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKVIAA 66 89****************************************************** PP TIGR00700 58 vkrqveelthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavki 113 v +q+++ltht+fqv+ ye yve+ ek+na Pg kk++l+++G+eaven++ki lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 67 VTEQLNKLTHTCFQVLAYEPYVEVCEKINAKVPGDFAKKTLLVTTGSEAVENSIKI 122 ******************************************************** PP TIGR00700 114 arkytgrpgvvafsrgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrd 169 ar+ tgr gv+af++++hGrt +t+ lt+kv Py G+G +++ ++ra +p ++++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 123 ARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHG 178 *******************************************************9 PP TIGR00700 170 ialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelvaavas 225 + dd +a+ie++f+ d e++++aa+++ePvqGeGGf v++ke+++ ++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 179 VSI------DDSIASIERIFKNDAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRA 228 877......88899****************************************** PP TIGR00700 226 lckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGra 281 lc++hgi+liadevqtG rtG++fa+e +++ dl t aks+a+G+Pl+gv G+a lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 229 LCDQHGILLIADEVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKA 284 ******************************************************** PP TIGR00700 282 eildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielk 337 e +da apGglGGtyaG+P+a+aaalav+++ eee l +r++ +g+++ l ++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 285 EYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQ 340 ******************************************************** PP TIGR00700 338 eevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGn 392 ++ p+ig+vr lGamiavel + d+++P+aa + + a+a+ +Gl+ll++G +Gn lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 341 AKYPVIGEVRALGAMIAVELFeNGDSHKPNAAAVASVVAKARDKGLILLSCGTYGN 396 *******************9968899****************************** PP TIGR00700 393 iirlltPltisdelldeglkileaal 418 ++r+l Plt +de+ld+gl i+e+ + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_494 397 VLRVLVPLTSPDEQLDKGLAIIEECF 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.48 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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