Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate AO356_25585 AO356_25585 2-hydroxymuconic semialdehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25585 Length = 486 Score = 392 bits (1007), Expect = e-113 Identities = 196/483 (40%), Positives = 304/483 (62%), Gaps = 15/483 (3%) Query: 9 MLENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQE 68 M++++IDG+ + +Y+P+TGE V + G +E+ AV AA+EAFP W++ +E Sbjct: 1 MIKHWIDGREVESKDVFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFPKWANTPAKE 60 Query: 69 RSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSEC 128 R+R++ ++ +L+EQ++ + A+ E+ D G + + + IPR+ NF FFA C Sbjct: 61 RARLMRKLGELIEQNVPKLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEV-------C 113 Query: 129 TQMD-HL-----GCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSEL 182 T+MD H ++YT+ PVGV L+SPWN+P TWK AP +A GNT + K SEL Sbjct: 114 TRMDGHTYPVDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSEL 173 Query: 183 TSVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQL 242 + +TA L +L +AG+P GV+N++ G G G+ALV HP+V ISFTG T ++I Q Sbjct: 174 SPLTANELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQT 233 Query: 243 SAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSE 302 + KK S+ELGGK+P +IFEDA+L+ + A + + F+ GE C SRIF+Q+S+Y + Sbjct: 234 AG--LKKYSMELGGKSPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQ 291 Query: 303 FLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLS 362 F+ F ++ VG P DP +G++I++AH +KV Y+K L EGA + G + Sbjct: 292 FVAEFAARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPAN 351 Query: 363 LPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAAT 422 LPA G F+ PTV D+ ++ EEIFGPV C++PF E E ++ AN+ +YGLA+ Sbjct: 352 LPAHLSHGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASY 411 Query: 423 VWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKT 482 +W+ ++G+ HR+A +++G+V+ N +R+L PFGG+K SG GREG + S++ F EIK Sbjct: 412 IWTQDIGKAHRLAHGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKN 471 Query: 483 ITV 485 + + Sbjct: 472 VCI 474 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: 578 Number of extensions: 21 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: 486 Length adjustment: 34 Effective length of query: 453 Effective length of database: 452 Effective search space: 204756 Effective search space used: 204756 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