Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Length = 430 Score = 435 bits (1118), Expect = e-126 Identities = 219/416 (52%), Positives = 288/416 (69%), Gaps = 1/416 (0%) Query: 8 LNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAI 67 L ++R PRG+ DRA+ + LWDV+G+ Y DF GI VLN GH HP+V+ A+ Sbjct: 11 LLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAV 70 Query: 68 AAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHT 127 AQL++ +H +Q+V Y+ Y+ LA+R+ ++ Q K A FT+GAEAVENA+KIARAHT Sbjct: 71 QAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHT 130 Query: 128 GRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQA 187 R VIAF G FHGRTLLG LTG PYK FGPF +++H P+P+A GV+++ AL+A Sbjct: 131 NRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTSDMALKA 190 Query: 188 LEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFG 247 L+ L T + P RVAAII+EPVQG+GGF +AP +F++ LRA+ +HGIVLI DE+QTGFG Sbjct: 191 LDELLATQVAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFG 250 Query: 248 RTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVA 307 RTGK F H ++PDL+T+AKSLAGG+PLS V G+A IMDAPLPGGLGGTY GN L+ A Sbjct: 251 RTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCA 310 Query: 308 AAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFC-DPATG 366 AA AVI+ E+E+L R +LG++LRE LL + P + +VRG G M+A E D Sbjct: 311 AALAVIEAYEQEQLLARGEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELIKDDDAR 370 Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 P A+ +R+ A GL+++ CG Y NV+RFL PL +AQ D AL +L ALA Sbjct: 371 TPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQILDAALA 426 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: 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: 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 Pf1N1B4_4910 (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.17086.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 0.1 2e-165 536.4 0.1 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketogl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 536.4 0.1 2e-165 2e-165 2 419 .. 14 426 .. 13 427 .. 0.99 Alignments for each domain: == domain 1 score: 536.4 bits; conditional E-value: 2e-165 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveel 65 +r+++v++G+ ++ + ++ +a+g+el dvdG+r++d+ +gi+vln+Gh+hPkvv+av+ q++++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 14 QRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPKVVAAVQAQLQKV 77 79************************************************************** PP TIGR00700 66 thtafqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrg 129 h++fqvv y+ y++la++l+++ g + ka++++sGaeavenavkiar++t+r +v+af +g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 78 SHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVENAVKIARAHTNRSAVIAFRGG 141 **************************************************************** PP TIGR00700 130 fhGrtnltmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadv 193 fhGrt l +lt+ ++Pyk fGPfapev+++P+p yr+ ++ d l+a+++l ++v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 142 FHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTS------DMALKALDELLATQV 199 ***************************************9987......44566********** PP TIGR00700 194 eaeqvaavvlePvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaiehedd 257 ++e+vaa+++ePvqG+GGf ++ e+++a++ l +hgivli de+qtGf rtGk f +h + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 200 APERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVLILDEIQTGFGRTGKWFGFQHAGI 263 **************************************************************** PP TIGR00700 258 kPdlitvaksladGlPlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglier 321 +Pdl+tvaksla+GlPlsgvvG+aei+dap pGglGGty+Gn l++aaalav++ e+e l r lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 264 QPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGTYGGNALSCAAALAVIEAYEQEQLLAR 327 **************************************************************** PP TIGR00700 322 aeqigklvkdklielkeevpaigdvrglGamiavelv.dpdttePdaalaekiaaaalaaGlll 384 e +g+++++ l+ l++ p+igdvrg G m+a+el+ d d++ Pda l +++ +a+a Gll+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 328 GEALGERLREGLLRLQARYPRIGDVRGSGFMLAIELIkDDDARTPDADLNQRLIDEARAGGLLV 391 ***********************************998999*********************** PP TIGR00700 385 ltaGifGniirlltPltisdelldeglkileaala 419 + +G++ n++r+l+Pl+ s++++de+l+il aala lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 392 IKCGVYRNVLRFLAPLVTSEAQVDEALQILDAALA 426 ********************************997 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.95 // [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