Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AO356_26715 AO356_26715 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26715 Length = 430 Score = 434 bits (1117), Expect = e-126 Identities = 220/415 (53%), Positives = 285/415 (68%), Gaps = 1/415 (0%) Query: 8 LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67 L ++R PRG+ DRA+ A +WDV+G Y DF GI VLN GH HP+V+ A+ Sbjct: 11 LLRQRDQFVPRGLVTAHPLVIDRAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAV 70 Query: 68 AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127 AQL++ +H +Q+V Y+ Y+ L +R+ LV Q K ALFT+GAEAVENA+KIARAHT Sbjct: 71 QAQLQKVSHACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHT 130 Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187 RP VI+F G FHGRTLLG LTG PYK FGPF +++H P+P+A G S+E ALQA Sbjct: 131 NRPAVISFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSSEMALQA 190 Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247 L L T + P RVAAII+EPVQG+GGF +AP +F++ LR + +QHGIVLI DE+QTGFG Sbjct: 191 LNELLATQVAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFG 250 Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307 RTGK F H ++PDL+T+AKSLAGG+P+S V GRA IMDAPLPGGLGGTY GN L+ A Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCA 310 Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFC-DPATG 366 AA AVID E+E+L ER LG++LR+ LL + P + +VRG G M+A E D Sbjct: 311 AALAVIDAYEQEQLLERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIKDDEAR 370 Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421 P AE +++ +A L+++ CG + NV+RFL PL ++Q D AL +L AL Sbjct: 371 SPDAELTQQLIDQARVGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425 Lambda K H 0.321 0.136 0.400 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: 529 Number of extensions: 21 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: 423 Length of database: 430 Length adjustment: 32 Effective length of query: 391 Effective length of database: 398 Effective search space: 155618 Effective search space used: 155618 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 (21.9 bits) S2: 51 (24.3 bits)
Align candidate AO356_26715 AO356_26715 (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.2313.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-162 526.0 0.0 3.2e-162 525.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 AO356_26715 4-aminobutyrate amin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 AO356_26715 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 525.8 0.0 3.2e-162 3.2e-162 2 418 .. 14 425 .. 13 427 .. 0.99 Alignments for each domain: == domain 1 score: 525.8 bits; conditional E-value: 3.2e-162 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqvee 64 +r+++v++G+ ++ + ++ +a+gae+ dvdG r++d+ +gi+vln+Gh+hPkvv+av+ q+++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 14 QRDQFVPRGLVTAHPLVIDRAQGAEVWDVDGARYLDFVGGIGVLNIGHNHPKVVAAVQAQLQK 76 79************************************************************* PP TIGR00700 65 lthtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafs 127 + h++fqvv y+ y++l ++l+++ g + ka+l++sGaeavenavkiar++t+rp+v++f lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 77 VSHACFQVVAYKPYLDLVKRLCELVGGQQAYKAALFTSGAEAVENAVKIARAHTNRPAVISFR 139 *************************************************************** PP TIGR00700 128 rgfhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfv 190 +gfhGrt l +lt+ ++Pyk fGPfapev+++P+p yr+ ++ + l+a+++l lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 140 GGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGFSS------EMALQALNELLA 196 *****************************************9988......34578******* PP TIGR00700 191 adveaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaie 253 ++v++++vaa+++ePvqG+GGf ++ e+++a+++l ++hgivli de+qtGf rtGk f + lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 197 TQVAPDRVAAIIIEPVQGDGGFLSAPPEFLQALRTLTEQHGIVLILDEIQTGFGRTGKWFGFQ 259 *************************************************************** PP TIGR00700 254 heddkPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieee 316 h + +Pdl+tvaksla+GlP+sgvvGra+i+dap pGglGGty+Gn l++aaalav+d e+e lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 260 HAGIQPDLVTVAKSLAGGLPISGVVGRAHIMDAPLPGGLGGTYGGNALSCAAALAVIDAYEQE 322 *************************************************************** PP TIGR00700 317 glieraeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaal 378 l er + +g+++++ l+ l++ p+igdvrg G m+a+el+ d +++ Pda l++++ +a+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 323 QLLERGQVLGERLRQGLLRLQARHPRIGDVRGTGFMLAIELIkDDEARSPDAELTQQLIDQAR 385 ****************************************9978999**************** PP TIGR00700 379 aaGlllltaGifGniirlltPltisdelldeglkileaal 418 ll++ +G++ n++r+l+Pl+ ++++de+l ileaal lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26715 386 VGRLLVIKCGVHRNVLRFLAPLVTEESQIDEALTILEAAL 425 *************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (430 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: 00:00:00.01 # Mc/sec: 9.53 // [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