Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_011842390.1 RSPH17029_RS17535 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000015985.1:WP_011842390.1 Length = 442 Score = 190 bits (483), Expect = 7e-53 Identities = 147/427 (34%), Positives = 213/427 (49%), Gaps = 32/427 (7%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 PV AE E + D EGR Y+D +GG AV GH + V AA+ +QL +L+ Sbjct: 15 PVAAE-GEGCYILDAEGRRYLDGSGGAAVSCLGHSNAAVRAALHDQLDRLAFAHTGFFTS 73 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR------AATGRAGVIAFTGA 138 EP LA+ +A P ++ LV+ GSEAVE A+K+AR GR VIA + Sbjct: 74 EPAERLADRLAAAAPEGI-ERVYLVSGGSEAVEAALKLARQYFMEVGQPGRHRVIARRQS 132 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPC-ELHGVSEDDSIASIERIFKNDAQ 197 YHG T+ L G + L+ ++PC E G +ED+S+ + ++ + Sbjct: 133 YHGNTLGALAAGGNEWRRAQFAPLLVETSH--VSPCYEYRGRAEDESLEAYGLRVADELE 190 Query: 198 -------PQDIAAIIIEPVQGE-GGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRT 249 P+ + A + EPV G G +++R+R +CD+HG+LLI DEV G GRT Sbjct: 191 AEIQRLGPETVMAFVAEPVVGATAGAVPAVPGYLKRIREICDRHGVLLILDEVMCGMGRT 250 Query: 250 GTFFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGG----LGGTYAGSPI 304 G FA + G+ PD+ T AK +G G+ PI + + + DAIA G G TY G + Sbjct: 251 GHLFACAEDGVAPDMITIAKGLGAGYQPIGALLVQGRLYDAIAAGSGFFQHGHTYMGHAM 310 Query: 305 ACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGG 364 A AAA AVL E LL+ + G RL+ L+E +H +GD+RG G IEL Sbjct: 311 AAAAANAVLDEIEGRDLLQAVRRQGARLEGLLQERLGQHPHVGDIRGRGLFRGIELVADR 370 Query: 365 DTHK---PAAELVSKIVVRAREKGLILLSCGTYYNVIR-----FLMPVTIPDAQLEKGLA 416 +T + PA +L ++I A GLI G + +R P I +A+LE+ + Sbjct: 371 ETKEPFDPARKLHARIKAEAFAGGLICYPMGGTLDGVRGDHILLAPPFIISNAELEELVD 430 Query: 417 ILAECFD 423 L+ D Sbjct: 431 KLSGALD 437 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: 531 Number of extensions: 30 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: 442 Length adjustment: 32 Effective length of query: 394 Effective length of database: 410 Effective search space: 161540 Effective search space used: 161540 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 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