Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012631286.1 MNOD_RS39905 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000022085.1:WP_012631286.1 Length = 471 Score = 154 bits (390), Expect = 4e-42 Identities = 117/365 (32%), Positives = 171/365 (46%), Gaps = 25/365 (6%) Query: 47 SPKTFPVSAFAAA-SAAVLANDGPAALQYAASEGYAPLRQAIADFLPWDVDA-----DQI 100 S FPV A+ A + A L A L+Y +G LR A+ +L W DQ+ Sbjct: 119 SAADFPVLAWRRALNRASLRRT--ARLRYGDPQGSVALRTALQGYL-WRARGIRCTPDQV 175 Query: 101 LITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEPSVVAVASDDEGVLIDDL 160 +I GSQQ LDL A++L+D ++E P YL A AFT V + D +G+ D L Sbjct: 176 VIVNGSQQGLDLCARLLLDPGDPFVIENPGYLLARHAFTAAGGVAVPIPVDGDGLRTDAL 235 Query: 161 KAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDN 220 + AR YV P+ Q P G ++ ARR L+ AA ++ED+ G+ D Sbjct: 236 PS--------ARLAYVTPSHQFPLGSVLSAARRRTLLAWAARAGACIIEDDYDGEYRHDI 287 Query: 221 PPPAPLTARNPEGCIYMGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQR 280 P PL +PE IY+G+FSK L+P LRLG++V P + +AK+ D HTP Q Sbjct: 288 APIPPLQTLSPEAAIYVGTFSKTLSPTLRLGYLVVPTPMCRAFSEAKRLTDRHTPQLEQD 347 Query: 281 LVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFL--WVRLP 338 +AE++ +RHV +IR ++ +L AL E+ G V D G+ + W+ Sbjct: 348 ALAELLASGAYERHVRSIRRKNTERRAVLLQALADEL-GPAVTIAGADTGLHVVAWINGV 406 Query: 339 EGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTS----TVEQIATGIAALAA 394 L+ A V P + Y D +PR F+ + + G+A LA Sbjct: 407 AADRERALVAAARAAGVGLYPVSPLY-DPTEPRPAAAGFILGYAGLDADALRRGVAVLAT 465 Query: 395 AIRSH 399 + H Sbjct: 466 VMAEH 470 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: 427 Number of extensions: 19 Number of successful extensions: 2 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: 471 Length adjustment: 32 Effective length of query: 369 Effective length of database: 439 Effective search space: 161991 Effective search space used: 161991 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 10 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