Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate RR42_RS27835 RR42_RS27835 betaine-aldehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Cup4G11:RR42_RS27835 Length = 486 Score = 385 bits (990), Expect = e-111 Identities = 191/477 (40%), Positives = 298/477 (62%), Gaps = 3/477 (0%) Query: 9 MLENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQE 68 M++++I+GK + +++P+TGE V G+ E+ AAV AA+ AFP W++ +E Sbjct: 1 MIKHWINGKQVDSKDTFTTWNPATGEEIATVAAGGEAEVNAAVAAAKAAFPKWANTPAKE 60 Query: 69 RSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSEC 128 R+R++ ++ADL+ + + A E++D G +A IPR+ +NF FFA + Sbjct: 61 RARIMRRLADLITEHVPHLAALETQDTGLPIAQTGKQLIPRAAENFNFFAEVCVQMNGRT 120 Query: 129 TQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAW 188 +D ++YT+ PVGV LISPWN+P TWK+AP +A GNT + K SEL+ +TA Sbjct: 121 YPVDDQ-MLNYTLYQPVGVCALISPWNVPFMTATWKVAPCLALGNTAVLKMSELSPLTAD 179 Query: 189 MLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCK 248 L L +AGVP GV+N+V G G G+ALV HP+V +SFTG T +RI + + K Sbjct: 180 QLGMLALEAGVPAGVLNVVQGYGASAGDALVRHPDVRAVSFTGGTATGKRIIERAG--LK 237 Query: 249 KLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFV 308 K S+ELGGK+P ++F+DA+L+ + A + + F+ GE C SRIFVQ ++Y +F +F Sbjct: 238 KFSMELGGKSPVLVFDDADLERALDAALFTIFSINGERCTAGSRIFVQDTVYDDFAGKFA 297 Query: 309 EATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQ 368 E R+ +VG P+ +GA+I++ H EKV Y++ EGA I G LPA + Sbjct: 298 ERARRLRVGDPTSEQTHVGAMITQQHWEKVTGYIRLGEQEGATILAGGAERPSDLPAHLR 357 Query: 369 AGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNV 428 G F+ PTV+ ++++ EEIFGPV C++PF E++ + AN+ YGLA+ +W+ +V Sbjct: 358 NGNFVQPTVLANVENHMRVAQEEIFGPVACLIPFKGEDDGLAMANDTAYGLASYIWTQDV 417 Query: 429 GRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485 G+VHR+A+ +++G+V+ N +R+L PFGG K+SG GREG + S++ F E+K + + Sbjct: 418 GKVHRLARGIEAGMVFVNSQNVRDLRQPFGGTKASGTGREGGEFSFEVFAEVKNVCI 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: 618 Number of extensions: 23 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