Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Smeli:SM_b21301 Length = 794 Score = 360 bits (923), Expect = e-103 Identities = 205/467 (43%), Positives = 276/467 (59%), Gaps = 15/467 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FIN + + S K+F T P+TG+++ ++A G ++DV+ AV AAR A PW ++ Sbjct: 36 FINGAFVGSASGKSFDTFEPATGKLLAKIAHGGRDDVNAAVAAARKA---QGPWAKLSGH 92 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R R L LA LI+R +A +E LDNGKP + +D+ + + ++AGWA + Sbjct: 93 ARARHLYALARLIQRHARLIAVVEALDNGKPIRETRDIDIPLAARHFYHHAGWAQLQETE 152 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 + PVGV GQ+IPWNFP LM AWK+ PALA GN V++K AE TPLTAL Sbjct: 153 ----------FADQVPVGVVGQVIPWNFPFLMLAWKVAPALALGNSVILKPAEFTPLTAL 202 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 A L AG PPGV+N+V G G T GA I HED+DK+AFTGSTE+GR+I+ S Sbjct: 203 LFAELAAAAGLPPGVLNVVTGEGET-GALIVEHEDIDKIAFTGSTEVGRLIREKTAGSG- 260 Query: 280 KRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERS 339 K +TLELGGKSP I+ DAD+D AVE A++FNQGQ CCAGSR VQE + F +R Sbjct: 261 KSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVCCAGSRLLVQEGVAPVFHDRL 320 Query: 340 VARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQ 399 R ++ VG+P D + V Q ++I + G EGA + G F + Sbjct: 321 KRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVAEGASMHQPKIELPKGGSFFR 380 Query: 400 PTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYL 459 PT+ VQ +A EEIFGPV + F+T EE + AN+S YGLAA+V+++ + A ++ Sbjct: 381 PTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLANHSRYGLAASVWSETIGLALHV 440 Query: 460 SQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506 + L AG VWVN ++F A S FGG + SG GRE G G Y + K Sbjct: 441 AAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGGREGCYEYLKPK 487 Score = 102 bits (255), Expect = 4e-26 Identities = 84/286 (29%), Positives = 133/286 (46%), Gaps = 23/286 (8%) Query: 12 LGRRLLSAAATQAVPAPNQQPEVFC-------NQIFINNEWHDAVSRKTFPTVNPSTGEV 64 +GR+L +PAP Q F ++F+ + + P ++P G+V Sbjct: 490 MGRKL---RPEHGLPAPKQAAGDFAVPALDRTAKLFVGGKQARPDGNYSRPVLSPK-GKV 545 Query: 65 ICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLAD-LIERDRTYLAALE 123 I +V EG+++D+ AV AAR A S W A +R ++L +A+ L R + + Sbjct: 546 IGEVGEGNRKDIRNAVVAARGA----SGWSSATAHNRAQILYYIAENLSSRGAEFAGRIA 601 Query: 124 TLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTI--PIDGDFFSYTRHEPVGVCGQ 181 + + +++ + L Y WADKY G P+ G + EP GV G Sbjct: 602 AMTGAS--AANARAEVEASIARLFSYGAWADKYEGTVHQPPLRG--VALAMPEPQGVVGV 657 Query: 182 IIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGF 241 I P PLL + P +A GN VV +E PL A ++++ + PPGV+NIV G Sbjct: 658 ICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDFYSVLETSDVPPGVINIVTGS 717 Query: 242 GPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELG 287 A+A+H DVD + GS E+ +++ NLKR ++ G Sbjct: 718 AIELAKALAAHNDVDALWAFGSPELSTLVE-KLSVGNLKRTFVDYG 762 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: 1021 Number of extensions: 61 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 794 Length adjustment: 38 Effective length of query: 479 Effective length of database: 756 Effective search space: 362124 Effective search space used: 362124 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: 54 (25.4 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