Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate BWI76_RS03865 BWI76_RS03865 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Koxy:BWI76_RS03865 Length = 488 Score = 395 bits (1015), Expect = e-114 Identities = 198/476 (41%), Positives = 302/476 (63%), Gaps = 3/476 (0%) Query: 10 LENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQER 69 + ++I+GK + S Y + +P+TGEV V + G DE+ AV AA+EAFP W++ +ER Sbjct: 4 INHWINGKNVAGSDYFHTTNPATGEVLAEVASGGADEVNQAVAAAKEAFPKWANLPMKER 63 Query: 70 SRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT 129 +R++ ++ DL++Q++ E A E+ D G + + + IPR+ NF FFA + Sbjct: 64 ARLMRRLGDLIDQNVPEIAAMETADTGLPIHQTKNVLIPRASHNFEFFAEVCQQMNGKTY 123 Query: 130 QMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWM 189 +D ++YT+ PVGV L+SPWN+P TWK+AP +A GNT + K SEL+ +TA Sbjct: 124 PVDDK-MLNYTLVQPVGVCALVSPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTADR 182 Query: 190 LCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249 L +L +AG+P GV+N+V G G G+ALV H +V +SFTG T I + + KK Sbjct: 183 LGELALEAGIPAGVLNVVQGYGATAGDALVRHHDVRAVSFTGGTATGRNIMKNAG--LKK 240 Query: 250 LSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVE 309 S+ELGGK+P +IFEDA+++ + A + + F+ GE C SRIF+Q+SIY EF+KRF E Sbjct: 241 YSMELGGKSPVLIFEDADIERALDAALFTIFSINGERCTAGSRIFIQQSIYPEFVKRFAE 300 Query: 310 ATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQA 369 + +VG P+DP +GALIS+ H EKV Y++ + EGA + G LPA + Sbjct: 301 RANRLRVGDPTDPNTQVGALISQQHWEKVSGYIRLGIEEGATLLAGGADKPTDLPAHLRN 360 Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429 G F+ PTV+ D+ + EEIFGPV C++PF E E + AN+V+YGLA+ +W+ +V Sbjct: 361 GNFLRPTVLADVDNRMRVAQEEIFGPVACLLPFKDEAEGLRLANDVEYGLASYIWTQDVS 420 Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485 +V R+A+ +++G+V+ N +R+L PFGG+K+SG GREG + S++ F E+K + + Sbjct: 421 KVLRLARGIEAGMVFVNTQNVRDLRQPFGGVKASGTGREGGEYSFEVFAEMKNVCI 476 Lambda K H 0.319 0.133 0.404 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: 613 Number of extensions: 22 Number of successful extensions: 3 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: 487 Length of database: 488 Length adjustment: 34 Effective length of query: 453 Effective length of database: 454 Effective search space: 205662 Effective search space used: 205662 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: 52 (24.6 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