Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__azobra:AZOBR_RS19630 Length = 428 Score = 541 bits (1395), Expect = e-158 Identities = 269/424 (63%), Positives = 325/424 (76%), Gaps = 3/424 (0%) Query: 3 MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62 M N RR A PRG+ Y DRAENA LWDVEG + DFA GIAVLNTGHRHP+ Sbjct: 1 MSNQSFQDRRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPK 60 Query: 63 VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122 +++A+ AQL+RFTHT + PY+ +VTLAER+NALVP KTA FTTGAEAVENA+KI Sbjct: 61 IIEAVKAQLDRFTHTCAMVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKI 120 Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182 ARAHTGRPGVIAFSGAFHGRTLL MALTGKV PYK+GFGPFP+++YHAPFP+A GVS + Sbjct: 121 ARAHTGRPGVIAFSGAFHGRTLLAMALTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSVQ 180 Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242 +L+ALE LFK+D+D RVAAIIVEPVQGEGGF AP +F++ LR +CD++GI+LI DE+ Sbjct: 181 DSLKALEQLFKSDVDATRVAAIIVEPVQGEGGFNIAPPEFLQALRKICDENGILLIIDEI 240 Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302 QTGF RTGKMFA+ H VEPDL+TMAKSLAGG PLSAV+G+A IMDAP+PGG+GGTYAG+ Sbjct: 241 QTGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAVTGKAEIMDAPIPGGIGGTYAGS 300 Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQL--REHLLAQRKHCPAMAEVRGLGSMVAAEF 360 PLA AA AV+DVIEEEKL +RS LG+++ R +AQR + +VR LG M+A E Sbjct: 301 PLATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMAQRNTLSVIGDVRNLGGMIAMEL 360 Query: 361 C-DPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQ 419 D T +P+AE K + +A E GLVLL+CGTYGNVIR L PLT A D L ++ + Sbjct: 361 VKDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLDIIER 420 Query: 420 ALAE 423 +L E Sbjct: 421 SLEE 424 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: 587 Number of extensions: 18 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 391 Effective length of database: 396 Effective search space: 154836 Effective search space used: 154836 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 AZOBR_RS19630 AZOBR_RS19630 (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.6614.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-194 630.0 2.1 9e-194 629.8 2.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS19630 AZOBR_RS19630 4-aminobutyrate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.8 2.1 9e-194 9e-194 2 419 .. 9 423 .. 8 424 .. 0.98 Alignments for each domain: == domain 1 score: 629.8 bits; conditional E-value: 9e-194 TIGR00700 2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtaf 70 rr+aav++G++++++v++ +ae+ael dv+Gnr+id+a+giavln+Gh+hPk++eavk q++++tht+ lcl|FitnessBrowser__azobra:AZOBR_RS19630 9 RRNAAVPRGLANAMPVYVDRAENAELWDVEGNRFIDFAGGIAVLNTGHRHPKIIEAVKAQLDRFTHTCA 77 9******************************************************************** PP TIGR00700 71 qvvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltma 139 +v+pyes+v+lae+lna+ Pgs +kk++++++Gaeavenavkiar++tgrpgv+afs++fhGrt l+ma lcl|FitnessBrowser__azobra:AZOBR_RS19630 78 MVTPYESFVTLAERLNALVPGSTPKKTAFFTTGAEAVENAVKIARAHTGRPGVIAFSGAFHGRTLLAMA 146 ********************************************************************* PP TIGR00700 140 ltakvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqG 208 lt+kv Pyk+GfGPf++evy+aP+p yr+ ++ q+sl+ a+e+lf++dv+a +vaa+++ePvqG lcl|FitnessBrowser__azobra:AZOBR_RS19630 147 LTGKVVPYKVGFGPFPAEVYHAPFPNAYRGVSV--QDSLK----ALEQLFKSDVDATRVAAIIVEPVQG 209 ******************************999..66665....************************* PP TIGR00700 209 eGGfivpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgv 277 eGGf++++ e+++a++++c+e+gi+li de+qtGfartGk+faieh +++Pdl+t+aksla+G+Pls+v lcl|FitnessBrowser__azobra:AZOBR_RS19630 210 EGGFNIAPPEFLQALRKICDENGILLIIDEIQTGFARTGKMFAIEHSGVEPDLMTMAKSLAGGFPLSAV 278 ********************************************************************* PP TIGR00700 278 vGraeildapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdkliel..keevpaig 344 +G+aei+dap pGg+GGtyaG+Pla +aalavld+ieee li+r++++g+++ + ++ +++ +ig lcl|FitnessBrowser__azobra:AZOBR_RS19630 279 TGKAEIMDAPIPGGIGGTYAGSPLATTAALAVLDVIEEEKLIQRSNDLGERIAGRFRTMaqRNTLSVIG 347 ****************************************************998876611567789** PP TIGR00700 345 dvrglGamiavelv.dpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglk 412 dvr+lG mia+elv d +t+eP a l++++ a+a ++Gl+ll++G +Gn+ir+l Plt sd+l+degl+ lcl|FitnessBrowser__azobra:AZOBR_RS19630 348 DVRNLGGMIAMELVkDRGTKEPAAELTKALVAKAAEKGLVLLSCGTYGNVIRILVPLTASDALVDEGLD 416 **************999**************************************************** PP TIGR00700 413 ileaala 419 i+e +l+ lcl|FitnessBrowser__azobra:AZOBR_RS19630 417 IIERSLE 423 **99885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (428 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: 10.31 // [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