Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 409 bits (1052), Expect = e-118 Identities = 216/479 (45%), Positives = 294/479 (61%), Gaps = 4/479 (0%) Query: 37 NQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRM 96 +Q +I+ W DA TF T+NP+TG+ + +VA +DVD+AV AAR AFQ G W Sbjct: 21 SQAYIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAARKAFQSGV-WSDT 79 Query: 97 DASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKY 156 S R L RL+ LIE R LA LETLD GKP + D+ + +YA DK Sbjct: 80 PRSARKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGRTYAWYAEAIDKI 139 Query: 157 HGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPL 216 + + P + EP+GV ++PWN+PLLM +WK+ PALA GN VV+K AEQ+PL Sbjct: 140 YDEIAPTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGNSVVLKPAEQSPL 199 Query: 217 TALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGS 276 TAL +A L +EAG P GV N+VPG G AG A+ H DVD +AFTGST G+ +G Sbjct: 200 TALRLAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGSTATGKRFMEYSGQ 259 Query: 277 SNLKRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEF 335 SNLKRV LE GGKSP+I+ D D+D A + A +F NQG+ C AGSR +VQ IYD F Sbjct: 260 SNLKRVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGSRLYVQSGIYDAF 319 Query: 336 VERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA--AD 393 +E+ A A G+P D T G VD Q ++++ Y+ +G+ EGA+L GG A Sbjct: 320 MEKLEAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGARLRAGGKRAHTDS 379 Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453 G+++QPT+F +TI +EEIFGPV+ + +F++ EE + AN+S YGL + ++T +L Sbjct: 380 GGFYMQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSPYGLGSGLWTSNL 439 Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 +A+ +S+ LQAG VWVNCY PFGG K SGSGR+ + L YT++KT + + Sbjct: 440 SRAHRVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDKYTDLKTTWISL 498 Lambda K H 0.319 0.136 0.409 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: 603 Number of extensions: 23 Number of successful extensions: 4 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: 517 Length of database: 499 Length adjustment: 34 Effective length of query: 483 Effective length of database: 465 Effective search space: 224595 Effective search space used: 224595 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