Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate H281DRAFT_02621 H281DRAFT_02621 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Burk376:H281DRAFT_02621 Length = 447 Score = 184 bits (466), Expect = 6e-51 Identities = 134/391 (34%), Positives = 193/391 (49%), Gaps = 30/391 (7%) Query: 27 VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86 +A R + + D G YID GG AV GH HP+VI A+Q Q+ +L + EP Sbjct: 15 IAVRGDGIEIVDSTGTRYIDACGGAAVSCLGHSHPRVIEAIQRQVQQLPYAHTSFFTTEP 74 Query: 87 YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR------AATGRAGVIAFTGAYH 140 LA+ + + P + V+ GSEA+E A+K+AR R IA +YH Sbjct: 75 AEALADLLIEAAPRNL-GHVYFVSGGSEAMEAALKLARQYFVEKGQPERRHFIARRQSYH 133 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPC----ELHGVSEDDSIASIERIFKN-- 194 G T+ L + G + ++ + PC E D++ A +R+ Sbjct: 134 GNTLGALAIGGNAWRREPFLPILIEA--HHVTPCFAYREQQAGETDEAFA--QRLADELE 189 Query: 195 ----DAQPQDIAAIIIEPVQG-EGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRT 249 + Q +AA + E V G G + + +++RA+CD++G+LLI DEV +G GRT Sbjct: 190 AKILELGAQSVAAFVAETVVGATAGAVPPVREYFRKIRAVCDKYGVLLILDEVMSGMGRT 249 Query: 250 GTFFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGG----LGGTYAGSPI 304 G FA E+ G+ PD+ AK +G G+ PI EI + I G G TY G Sbjct: 250 GHLFACEEDGVSPDILAIAKGLGAGYQPIGATLVSNEIFNTIVGGSGFFQHGHTYIGHAT 309 Query: 305 ACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFE-- 362 ACAAAL V KV EE+LL+ +A GE+L+A LRE QA H IGDVRG G +EL + Sbjct: 310 ACAAALEVQKVIAEEQLLDNVKARGEQLRARLREWQANHPFIGDVRGRGLFTGVELVQDR 369 Query: 363 -GGDTHKPAAELVSKIVVRAREKGLILLSCG 392 P +L + I A ++GL++ G Sbjct: 370 ASKTAFDPKHKLHAIIKSEAMKRGLMVYPMG 400 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: 460 Number of extensions: 27 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 447 Length adjustment: 32 Effective length of query: 394 Effective length of database: 415 Effective search space: 163510 Effective search space used: 163510 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: 51 (24.3 bits)
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