Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate RR42_RS26850 RR42_RS26850 hypothetical protein
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Cup4G11:RR42_RS26850 Length = 447 Score = 192 bits (487), Expect = 2e-53 Identities = 135/389 (34%), Positives = 196/389 (50%), Gaps = 26/389 (6%) Query: 27 VAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEP 86 VA + + D G+ YID +GG AV GH HP+VI A+++Q L++ E Sbjct: 15 VAVAGKGIELVDSNGKHYIDASGGAAVSCLGHGHPRVIEAIKQQADSLAYAHTSFFTTEV 74 Query: 87 YIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR------AATGRAGVIAFTGAYH 140 ELA +A+ PGD V+ GSEAVE A+K+AR T R IA +YH Sbjct: 75 SEELARTLAQAAPGDL-NHVYFVSGGSEAVEAALKLARQYFVEIGQTQRRHFIARRQSYH 133 Query: 141 GRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHG---VSEDDSIASIERIFKNDAQ 197 G T+ L + G + L+ +APC + E D + + +A+ Sbjct: 134 GNTLGALAIGGNAWRREPFLPLLVPA--HHVAPCYAYRDQEAGETDQQYAQRLADELEAK 191 Query: 198 -----PQDIAAIIIEPVQGE-GGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGT 251 P +AA + E V G G +++R+RA+CD++G+LLI DE+ +G GRTG Sbjct: 192 ILELGPHSVAAFVAETVVGATAGAVPPVADYLRRVRAVCDKYGVLLILDEIMSGMGRTGY 251 Query: 252 FFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGG----LGGTYAGSPIAC 306 FA E+ G+VPD+ T AK + G+ PI + + I DA+ G G TY G AC Sbjct: 252 LFACEEDGVVPDIVTIAKGLAAGYQPIGAMISSSRIYDAVVGGSGFFQHGHTYIGHATAC 311 Query: 307 AAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELF---EG 363 AAALAV + E+ LLE A G +L+A LRE H +GD+RG G V +E E Sbjct: 312 AAALAVQRTIAEDCLLENVLARGGQLRARLRETLGDHPNVGDIRGRGLFVGVEFVAERET 371 Query: 364 GDTHKPAAELVSKIVVRAREKGLILLSCG 392 T PA ++ +++ A + GL++ G Sbjct: 372 KATLDPALKMHARLKSTAMQNGLLIYPMG 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: 449 Number of extensions: 24 Number of successful extensions: 5 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: 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