Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011840643.1 RSPH17029_RS04315 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000015985.1:WP_011840643.1 Length = 425 Score = 529 bits (1362), Expect = e-155 Identities = 256/420 (60%), Positives = 312/420 (74%) Query: 3 MKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPR 62 M N ++++RRT A RGVG+ YADRA NA +WD+EGR Y DFAAGIAV+NTGH HP+ Sbjct: 1 MLNADVSRRRTEAVSRGVGMQTQIYADRALNAEIWDIEGRRYIDFAAGIAVVNTGHCHPK 60 Query: 63 VMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKI 122 VM A+A Q+ RFTHT +Q++PY+ Y+ LAER+NA P KT TTGAE+VENAIKI Sbjct: 61 VMAAVAEQMGRFTHTCHQVLPYENYIRLAERLNAAAPGDFAKKTVFVTTGAESVENAIKI 120 Query: 123 ARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTE 182 AR HTGR V+AF G FHGRT + M+LTGKV PYK GFG ++YH PFP ALHG+STE Sbjct: 121 ARIHTGRSAVVAFGGGFHGRTFMTMSLTGKVEPYKKGFGTMMPEVYHVPFPQALHGISTE 180 Query: 183 RALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEV 242 A+ AL LFK D+DP RVAAII EPVQGEGGF AP D +R +R +CD HGIV+IADEV Sbjct: 181 EAMAALARLFKADLDPGRVAAIIFEPVQGEGGFYPAPPDLVRAIRQLCDAHGIVMIADEV 240 Query: 243 QTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGN 302 QTGF RTG +FAM +DV PDL+TMAK L GG+P++AV+GRA IMDA PGGLGGTY GN Sbjct: 241 QTGFARTGTLFAMHGYDVAPDLVTMAKGLGGGLPIAAVTGRAEIMDAAHPGGLGGTYGGN 300 Query: 303 PLAVAAAHAVIDVIEEEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCD 362 PL +AAAHAV+DVIEEE LC R+ LG +L++ L R P +A++RG G MV AEF D Sbjct: 301 PLGIAAAHAVLDVIEEENLCARATELGSRLKQKLAEIRATAPEIADIRGPGFMVGAEFAD 360 Query: 363 PATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 P + P A RV+ AL+ GL+LLTCG +GNVIRFL P+TIP+ F AL +L ++A Sbjct: 361 PGSKAPDAGFTNRVREEALKRGLILLTCGVHGNVIRFLAPITIPEPHFAEALEILEASVA 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: 606 Number of extensions: 30 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: 425 Length adjustment: 32 Effective length of query: 391 Effective length of database: 393 Effective search space: 153663 Effective search space used: 153663 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 WP_011840643.1 RSPH17029_RS04315 (4-aminobutyrate--2-oxoglutarate transaminase)
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.461121.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-182 593.0 4.2 1.5e-182 592.8 4.2 1.0 1 NCBI__GCF_000015985.1:WP_011840643.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015985.1:WP_011840643.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 592.8 4.2 1.5e-182 1.5e-182 1 419 [. 8 420 .. 8 421 .. 0.99 Alignments for each domain: == domain 1 score: 592.8 bits; conditional E-value: 1.5e-182 TIGR00700 1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvv 73 +rr++avs+Gvg++++++a +a +ae+ d++G+r+id+aagiav+n+Gh hPkv++av +q+ ++tht++qv+ NCBI__GCF_000015985.1:WP_011840643.1 8 RRRTEAVSRGVGMQTQIYADRALNAEIWDIEGRRYIDFAAGIAVVNTGHCHPKVMAAVAEQMGRFTHTCHQVL 80 599********************************************************************** PP TIGR00700 74 pyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkP 146 pye y+ lae+lna aPg kk+v++++Gae+vena+kiar +tgr +vvaf +gfhGrt++tm+lt+kv P NCBI__GCF_000015985.1:WP_011840643.1 81 PYENYIRLAERLNAAAPGDFAKKTVFVTTGAESVENAIKIARIHTGRSAVVAFGGGFHGRTFMTMSLTGKVEP 153 ************************************************************************* PP TIGR00700 147 ykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakel 219 yk GfG + pevy++P+p +++i++ ++ +aa+ +lf+ad+++ +vaa+++ePvqGeGGf ++ +l NCBI__GCF_000015985.1:WP_011840643.1 154 YKKGFGTMMPEVYHVPFPQALHGIST------EEAMAALARLFKADLDPGRVAAIIFEPVQGEGGFYPAPPDL 220 ************************99......44567************************************ PP TIGR00700 220 vaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGgl 292 v a+++lc+ hgiv+iadevqtGfartG+lfa++ +d+ Pdl+t+ak+l +GlP+++v+Graei+da++pGgl NCBI__GCF_000015985.1:WP_011840643.1 221 VRAIRQLCDAHGIVMIADEVQTGFARTGTLFAMHGYDVAPDLVTMAKGLGGGLPIAAVTGRAEIMDAAHPGGL 293 ************************************************************************* PP TIGR00700 293 GGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiavelvdpdtteP 365 GGty+GnPl++aaa+avld+ieee l+ ra ++g ++k+kl e++++ p i+d+rg G m+ e+ dp+++ P NCBI__GCF_000015985.1:WP_011840643.1 294 GGTYGGNPLGIAAAHAVLDVIEEENLCARATELGSRLKQKLAEIRATAPEIADIRGPGFMVGAEFADPGSKAP 366 ************************************************************************* PP TIGR00700 366 daalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaala 419 da+ ++++ ++al++Gl+llt+G++Gn+ir+l+P+ti++ + e+l+ilea++a NCBI__GCF_000015985.1:WP_011840643.1 367 DAGFTNRVREEALKRGLILLTCGVHGNVIRFLAPITIPEPHFAEALEILEASVA 420 **************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (420 nodes) Target sequences: 1 (425 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17.00 // [ok]
This GapMind analysis is from Apr 10 2024. 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