Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__BFirm:BPHYT_RS22435 Length = 427 Score = 602 bits (1552), Expect = e-177 Identities = 294/421 (69%), Positives = 342/421 (81%) Query: 3 MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62 MKN EL R+ ATPRGVGVMCDFYA+RAENA LWDVEGR + DFAAGIAV NTGHRHP+ Sbjct: 1 MKNAELKSRKDAATPRGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPK 60 Query: 63 VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122 ++ AI QL+ FTHTAYQIVPY YV LAE++N P KTA FTTGAEAVENAIKI Sbjct: 61 ILAAIRDQLDHFTHTAYQIVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKI 120 Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182 ARA TGRPGVIAF+G FHGRTL+GMALTGKVAPYKIGFGPFPSD++HAPFP+ LHGV+T Sbjct: 121 ARAATGRPGVIAFTGGFHGRTLMGMALTGKVAPYKIGFGPFPSDVFHAPFPNPLHGVTTA 180 Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242 +L+A+E LFK DIDP RVAAII EPVQGEGGF APA+F+R LR +C++HGI+LIADEV Sbjct: 181 DSLKAIEFLFKADIDPKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEV 240 Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302 QTGF RTGK+FAM H+DV PDL+T+AKSLAGGMPLS V GRA +MDA PGGLGGTYAGN Sbjct: 241 QTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGN 300 Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362 PLAVAAAHAV+D+I+EEKLCER+ LG +++ L+A + P +A+VRG G MVA EFC Sbjct: 301 PLAVAAAHAVLDIIDEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGGMVAVEFCK 360 Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 +P AE KRVQTRALE GL+LL CG Y NV+RFL+PLTI A FD A+A+L + Sbjct: 361 AGGTEPDAEFTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIK 420 Query: 423 E 423 + Sbjct: 421 D 421 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: 645 Number of extensions: 17 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: 423 Length of database: 427 Length adjustment: 32 Effective length of query: 391 Effective length of database: 395 Effective search space: 154445 Effective search space used: 154445 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 BPHYT_RS22435 BPHYT_RS22435 (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.11288.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-199 648.7 1.0 1.8e-199 648.5 1.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS22435 BPHYT_RS22435 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 648.5 1.0 1.8e-199 1.8e-199 2 420 .] 9 421 .. 8 421 .. 0.99 Alignments for each domain: == domain 1 score: 648.5 bits; conditional E-value: 1.8e-199 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafq 71 r++aa+++Gvgv+++++a +ae+ael dv+G+r+id+aagiav n+Gh+hPk+++a++ q++++thta+q lcl|FitnessBrowser__BFirm:BPHYT_RS22435 9 RKDAATPRGVGVMCDFYAERAENAELWDVEGRRFIDFAAGIAVCNTGHRHPKILAAIRDQLDHFTHTAYQ 78 899******************************************************************* PP TIGR00700 72 vvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmalt 141 +vpy syvelaekln+ aPg ++kk++++++Gaeavena+kiar+ tgrpgv+af++gfhGrt + malt lcl|FitnessBrowser__BFirm:BPHYT_RS22435 79 IVPYASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARAATGRPGVIAFTGGFHGRTLMGMALT 148 ********************************************************************** PP TIGR00700 142 akvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGG 211 +kv+PykiGfGPf+++v++aP+p ++++ ++ d l+aie lf+ad+++++vaa+++ePvqGeGG lcl|FitnessBrowser__BFirm:BPHYT_RS22435 149 GKVAPYKIGFGPFPSDVFHAPFPNPLHGVTT------ADSLKAIEFLFKADIDPKRVAAIIFEPVQGEGG 212 ****************************998......34677**************************** PP TIGR00700 212 fivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGra 281 f ++ e+v a+++lc+ehgi+liadevqtGfartGklfa++h+d++Pdl+tvaksla+G+Plsgv+Gra lcl|FitnessBrowser__BFirm:BPHYT_RS22435 213 FYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHHYDVVPDLMTVAKSLAGGMPLSGVIGRA 282 ********************************************************************** PP TIGR00700 282 eildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGa 351 +++da+apGglGGtyaGnPlavaaa+avldii+ee l+era +g +vk kli l+ vp+i+dvrg G lcl|FitnessBrowser__BFirm:BPHYT_RS22435 283 DVMDAAAPGGLGGTYAGNPLAVAAAHAVLDIIDEEKLCERATLLGDRVKAKLIALQSDVPQIADVRGPGG 352 ********************************************************************** PP TIGR00700 352 miavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaalad 420 m+ave+ +++ tePda +++++++al++Gllll +G++ n++r+l Plti d+ +de++ ile++++d lcl|FitnessBrowser__BFirm:BPHYT_RS22435 353 MVAVEFCKAGGTEPDAEFTKRVQTRALERGLLLLVCGVYSNVVRFLFPLTIQDAVFDEAMAILEDVIKD 421 *****************************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (427 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: 10.95 // [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