Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Cup4G11:RR42_RS26160 Length = 424 Score = 719 bits (1856), Expect = 0.0 Identities = 354/420 (84%), Positives = 383/420 (91%) Query: 3 MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62 MKNLELNQRR LATPRGVGVMCDFYADRAENATLWDVEGR YTDFA GIAVLNTGHRHPR Sbjct: 1 MKNLELNQRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPR 60 Query: 63 VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122 VMQA+ AQLERFTHTAYQIVPY+ YV LAERINALVPI GL KTALFTTGAEAVENA+KI Sbjct: 61 VMQAVIAQLERFTHTAYQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKI 120 Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182 ARAHTGRPGVIAFSG FHGRTLLGMALTGKVAPYK+GFGPFPSDIYHAPFP LHGVSTE Sbjct: 121 ARAHTGRPGVIAFSGGFHGRTLLGMALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVSTE 180 Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242 +++QALE LFKTDIDP RVAAII+EPVQGEGGF AP DFM+ LRA+CD+HGI+LIADEV Sbjct: 181 QSIQALESLFKTDIDPQRVAAIIIEPVQGEGGFHPAPVDFMQTLRALCDKHGILLIADEV 240 Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302 QTGFGRTGK+FAMSH+ V PDLITMAKSLAGGMPLSAV GRA+IMDAPLPGGLGGTYAGN Sbjct: 241 QTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSAVCGRASIMDAPLPGGLGGTYAGN 300 Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362 PLAVAAAHAVI+ IE+E+LCER+ +LG+QL+ L + CP +A++RGLGSMVA EF D Sbjct: 301 PLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIADIRGLGSMVAVEFHD 360 Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 PATGQPSAE AKRVQ RA+EAGL+LLTCGTYGN IRFLYPLTIPQAQFDAAL VLT+ LA Sbjct: 361 PATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVLTKVLA 420 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: 718 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: 423 Length of database: 424 Length adjustment: 32 Effective length of query: 391 Effective length of database: 392 Effective search space: 153272 Effective search space used: 153272 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 RR42_RS26160 RR42_RS26160 (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.26529.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-195 634.4 1.0 3.9e-195 634.2 1.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS26160 RR42_RS26160 4-aminobutyrate ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS26160 RR42_RS26160 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 634.2 1.0 3.9e-195 3.9e-195 1 419 [. 8 420 .. 8 421 .. 0.99 Alignments for each domain: == domain 1 score: 634.2 bits; conditional E-value: 3.9e-195 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthta 69 qrra a+++Gvgv+++++a +ae+a+l dv+G+++ d+a+giavln+Gh+hP+v++av q+e++thta lcl|FitnessBrowser__Cup4G11:RR42_RS26160 8 QRRALATPRGVGVMCDFYADRAENATLWDVEGRQYTDFACGIAVLNTGHRHPRVMQAVIAQLERFTHTA 76 79******************************************************************* PP TIGR00700 70 fqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltm 138 +q+vpyesyv+lae++na+ P g kk++l+++Gaeavenavkiar++tgrpgv+afs+gfhGrt l m lcl|FitnessBrowser__Cup4G11:RR42_RS26160 77 YQIVPYESYVALAERINALVPIDGLKKTALFTTGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTLLGM 145 ********************************************************************* PP TIGR00700 139 altakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvq 207 alt+kv+Pyk+GfGPf++++y+aP+p d+++ ++ ++ ++a+e+lf++d+++++vaa+++ePvq lcl|FitnessBrowser__Cup4G11:RR42_RS26160 146 ALTGKVAPYKVGFGPFPSDIYHAPFPCDLHGVST------EQSIQALESLFKTDIDPQRVAAIIIEPVQ 208 *******************************998......45678************************ PP TIGR00700 208 GeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsg 276 GeGGf ++ +++++++ lc++hgi+liadevqtGf rtGklfa+ h+ + Pdlit+aksla+G+Pls+ lcl|FitnessBrowser__Cup4G11:RR42_RS26160 209 GEGGFHPAPVDFMQTLRALCDKHGILLIADEVQTGFGRTGKLFAMSHYPVAPDLITMAKSLAGGMPLSA 277 ********************************************************************* PP TIGR00700 277 vvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigd 345 v Gra i+dap pGglGGtyaGnPlavaaa+av+++ie+e l+era +gk +k l ++ ++ p i+d lcl|FitnessBrowser__Cup4G11:RR42_RS26160 278 VCGRASIMDAPLPGGLGGTYAGNPLAVAAAHAVIETIEQERLCERATALGKQLKAALQQASQTCPGIAD 346 ********************************************************************* PP TIGR00700 346 vrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkil 414 +rglG+m+ave+ dp t++P+a la++++ +a +aGl+llt+G +Gn ir+l+Plti+ +++d++l +l lcl|FitnessBrowser__Cup4G11:RR42_RS26160 347 IRGLGSMVAVEFHDPATGQPSAELAKRVQLRAMEAGLILLTCGTYGNTIRFLYPLTIPQAQFDAALVVL 415 ********************************************************************* PP TIGR00700 415 eaala 419 +++la lcl|FitnessBrowser__Cup4G11:RR42_RS26160 416 TKVLA 420 99886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (424 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: 00:00:00.01 # Mc/sec: 11.88 // [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