Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 344 bits (883), Expect = 4e-99 Identities = 187/485 (38%), Positives = 279/485 (57%), Gaps = 14/485 (2%) Query: 11 ENFIGGKFLPC--NSYIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQE 68 +N+IGGKF+ +Y D+ P G+V+ K +S KE++E AV+AA EAF WS S E Sbjct: 15 DNYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTE 74 Query: 69 RSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSEC 128 RS++LN++A +E +LE LA E+ D GK + D+P V +FR+FA Sbjct: 75 RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134 Query: 129 TQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAW 188 +++ + V P+G+ I PWN PL + WK+APA+AAGN V+ KP+E T V+ Sbjct: 135 SELDQ-NTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIM 193 Query: 189 MFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCK 248 + +L+ +PPGV+N+V G G +G ALV++P+V +FTGS PT + Q + + Sbjct: 194 VLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENII 252 Query: 249 KLSLELGGKNPAIIF------EDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSE 302 ++LELGGK+P I F +DA L++ + V + NQGEIC C SR+ +Q IY + Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEK 311 Query: 303 FLKRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLS 362 F+ + +E T+ K+G P D + MGA SK EK+ +Y+ + EGA +L G +++ Sbjct: 312 FIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE-- 369 Query: 363 LPLRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAAT 422 LP GY++ PT+ ++ R EEIFGPV V F + EE I AN YGL A Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428 Query: 423 VWSKDVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKT 482 VW++D +++V + +Q+G VW N + PFGG K SG+GRE K + + K Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKN 488 Query: 483 ITIKY 487 + I Y Sbjct: 489 MLISY 493 Lambda K H 0.319 0.134 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: 531 Number of extensions: 20 Number of successful extensions: 5 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: 501 Length adjustment: 34 Effective length of query: 453 Effective length of database: 467 Effective search space: 211551 Effective search space used: 211551 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