Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012061774.1 SMED_RS24200 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000017145.1:WP_012061774.1 Length = 491 Score = 130 bits (326), Expect = 1e-34 Identities = 106/360 (29%), Positives = 168/360 (46%), Gaps = 16/360 (4%) Query: 44 GLPSPKTFPVSAFAAASAAVLANDGPAAL--QYAASEGYAPLRQAIADFLPWD---VDAD 98 G P F ++A+ + L + + +AAS+ + + LP D Sbjct: 137 GQMDPSLFDLTAWRDCARRALGREDFELMAGDFAASDDVQLVNYICSRTLPGRGIRASPD 196 Query: 99 QILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVLID 158 +IL+T G+Q AL ++ ++L+ + S + E P + + V + D EG+ Sbjct: 197 EILVTVGAQNALWIVIQLLLRQGSHAVCENPCHPDMSASLRLSGAEVTVIDVDKEGLPPT 256 Query: 159 DLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDLWF 218 L DK ++V P+ +PTG TM RRAAL++AAA + +VED+ ++ F Sbjct: 257 ALP-------DKVDAVFVTPSHHSPTGATMPLDRRAALLEAAASKDFIIVEDDYEFEMSF 309 Query: 219 DNPPPAPLTARNPEGCI-YMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGY 277 PP L A + G + Y+GSFSK L PGLRLG++VAP AV + + H PG+ Sbjct: 310 LAPPSPALKAFDRSGRVFYIGSFSKSLFPGLRLGYLVAPAAVIREARALRALMLRHPPGH 369 Query: 278 NQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRL 337 QR A + D + +R Y ++ M AAL AGL + + GG W+ Sbjct: 370 LQRTAAYFLALGHYDAVLHRMREEYHRRHIIMAAALRD--AGLRIAGSAAFGGTSFWIEG 427 Query: 338 PEGMSAIELLPQAVERNVAFVPGAAFYADNADP-RTLRLSFVTSTVEQIATGIAALAAAI 396 P+ + A L+ V G+ F+ + P R R+ + + +IA G+A AA I Sbjct: 428 PDDLDADLLMNALRLEGVLIESGSPFFPKDDGPCRFFRMGYSSIARSRIADGVALTAARI 487 Lambda K H 0.318 0.134 0.392 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: 441 Number of extensions: 22 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: 401 Length of database: 491 Length adjustment: 32 Effective length of query: 369 Effective length of database: 459 Effective search space: 169371 Effective search space used: 169371 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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