Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS05420 Length = 426 Score = 627 bits (1617), Expect = 0.0 Identities = 305/423 (72%), Positives = 360/423 (85%), Gaps = 2/423 (0%) Query: 1 MTMK--NLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGH 58 MT K N EL QR+ ATPRGVGVMCDFYA+RA NA LWDVEGR + DFAAGIAVLNTGH Sbjct: 1 MTSKANNQELQQRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGH 60 Query: 59 RHPRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVEN 118 RHP+++ A+ AQ+++FTHTAYQIVPY YV LAERIN L P KTA F+TGAEAVEN Sbjct: 61 RHPKLLDAMRAQMDKFTHTAYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVEN 120 Query: 119 AIKIARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHG 178 AIKIARAHTGRPGVIAF+G FHGRT++GMALTGKVAPYK+GFGPFP D++HAP+PSALHG Sbjct: 121 AIKIARAHTGRPGVIAFAGGFHGRTMMGMALTGKVAPYKLGFGPFPGDVFHAPYPSALHG 180 Query: 179 VSTERALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLI 238 +++E AL+A++GLFK+DI+ RVAAII+EPVQGEGGF AAPADFMRGLRA+CD+HGI+LI Sbjct: 181 ITSEDALEAVKGLFKSDIEAKRVAAIILEPVQGEGGFYAAPADFMRGLRALCDEHGILLI 240 Query: 239 ADEVQTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGT 298 ADEVQ+G+GRTGK+FAM H+DV PDL+TMAKSLAGGMPLSAV+GRA IMDAP PGGLGGT Sbjct: 241 ADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGMPLSAVNGRAEIMDAPAPGGLGGT 300 Query: 299 YAGNPLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAA 358 YAGNPLA+A+A AV+DV+EEE+L R LG +L+EHL R P +AEVRG+G+MVA Sbjct: 301 YAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSVPQIAEVRGVGAMVAV 360 Query: 359 EFCDPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLT 418 EF DPATG+P AE+ K+VQ AL GL+LLTCG+YGNVIRFL+PLTIP D AL +L Sbjct: 361 EFADPATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMDEALGILA 420 Query: 419 QAL 421 +A+ Sbjct: 421 KAI 423 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: 671 Number of extensions: 18 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: 426 Length adjustment: 32 Effective length of query: 391 Effective length of database: 394 Effective search space: 154054 Effective search space used: 154054 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 HSERO_RS05420 HSERO_RS05420 (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.16505.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-197 640.7 0.4 5.2e-197 640.4 0.4 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS05420 HSERO_RS05420 4-aminobutyrate am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS05420 HSERO_RS05420 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.4 0.4 5.2e-197 5.2e-197 1 418 [. 12 423 .. 12 425 .. 0.99 Alignments for each domain: == domain 1 score: 640.4 bits; conditional E-value: 5.2e-197 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveeltht 68 qr++aa+++Gvgv+++++a +a +ael dv+G+r+id+aagiavln+Gh+hPk+++a++ q++++tht lcl|FitnessBrowser__HerbieS:HSERO_RS05420 12 QRKNAATPRGVGVMCDFYAERAANAELWDVEGRRFIDFAAGIAVLNTGHRHPKLLDAMRAQMDKFTHT 79 7999**************************************************************** PP TIGR00700 69 afqvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnl 136 a+q+vpy syvelae++n+++Pg +kk++++++Gaeavena+kiar++tgrpgv+af +gfhGrt + lcl|FitnessBrowser__HerbieS:HSERO_RS05420 80 AYQIVPYASYVELAERINRLTPGNYPKKTAFFSTGAEAVENAIKIARAHTGRPGVIAFAGGFHGRTMM 147 ******************************************************************** PP TIGR00700 137 tmaltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvle 204 malt+kv+Pyk+GfGPf+++v++aP+p+ +++i++ ++ l+a++ lf++d+ea++vaa++le lcl|FitnessBrowser__HerbieS:HSERO_RS05420 148 GMALTGKVAPYKLGFGPFPGDVFHAPYPSALHGITS--ED----ALEAVKGLFKSDIEAKRVAAIILE 209 *********************************988..55....556********************* PP TIGR00700 205 PvqGeGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGl 272 PvqGeGGf ++ +++ ++ lc+ehgi+liadevq+G+ rtGklfa+eh+d+ Pdl+t+aksla+G+ lcl|FitnessBrowser__HerbieS:HSERO_RS05420 210 PVQGEGGFYAAPADFMRGLRALCDEHGILLIADEVQSGYGRTGKLFAMEHYDVLPDLMTMAKSLAGGM 277 ******************************************************************** PP TIGR00700 273 PlsgvvGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeev 340 Pls+v Graei+dapapGglGGtyaGnPla+a+alavld++eee l+ r +++g ++++l el+ +v lcl|FitnessBrowser__HerbieS:HSERO_RS05420 278 PLSAVNGRAEIMDAPAPGGLGGTYAGNPLAIASALAVLDVMEEEQLVTRGQRLGDKLQEHLKELRSSV 345 ******************************************************************** PP TIGR00700 341 paigdvrglGamiavelvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelld 408 p+i++vrg Gam+ave+ dp t++Pda ++k++++al++Gllllt+G +Gn+ir+l Plti+d+ +d lcl|FitnessBrowser__HerbieS:HSERO_RS05420 346 PQIAEVRGVGAMVAVEFADPATGKPDAEYTKKVQQHALNNGLLLLTCGSYGNVIRFLFPLTIPDTVMD 413 ******************************************************************** PP TIGR00700 409 eglkileaal 418 e+l il +a+ lcl|FitnessBrowser__HerbieS:HSERO_RS05420 414 EALGILAKAI 423 ******9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (426 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: 7.66 // [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