Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_900105005.1:WP_090271605.1 Length = 417 Score = 287 bits (734), Expect = 5e-82 Identities = 153/396 (38%), Positives = 235/396 (59%), Gaps = 8/396 (2%) Query: 22 QIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQV 81 Q V AER E + +G+ Y+DF GI V +TGH HP V+AA +EQ+GKL H + Sbjct: 10 QSSKVCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTT 69 Query: 82 LAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHG 141 + ++P ++LAE + ++P D +GSEAVE A+++AR AT RA VI F G +HG Sbjct: 70 VTHQPMLDLAERLVGKMP-DGIDSVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHG 128 Query: 142 RTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCEL-HGVSEDDS----IASIERIFKNDA 196 RTM +T M G+ A P +G SE+++ +A ++ I K Sbjct: 129 RTMGAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQT 188 Query: 197 QPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATE 256 P+D AA++IEPVQGE G+Y + +FMQ L C QHGILL+ DE+Q G GR+G F++ + Sbjct: 189 APEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQ 248 Query: 257 QLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVF 316 GI PD+ AK + GFP+S +A +M G GGTY + ++CAAALA L+V Sbjct: 249 HFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVM 308 Query: 317 EEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSK 376 + E L+ + A G++L L+ ++ ++ + D+RG G M+ +E+ + D KP A+L + Sbjct: 309 DNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KPLADLAAS 366 Query: 377 IVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 + + E+GL+LL CGT +IR+L P+ + +A+++ Sbjct: 367 LTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVD 402 Lambda K H 0.319 0.137 0.393 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: 402 Number of extensions: 15 Number of successful extensions: 4 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: 426 Length of database: 417 Length adjustment: 32 Effective length of query: 394 Effective length of database: 385 Effective search space: 151690 Effective search space used: 151690 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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