Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Marino:GFF3202 Length = 533 Score = 363 bits (932), Expect = e-105 Identities = 205/479 (42%), Positives = 283/479 (59%), Gaps = 20/479 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 +I EW V + F + P TG VIC++ ED+D A+ AA A W + + Sbjct: 49 YIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKA---APAWGKTSPT 105 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++AD IE + LA ET DNGK + D+ + RY+AG G Sbjct: 106 ERSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQEGH 165 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 ID + +Y HEP+GV GQIIPWNFP+LM AWKLGP LA GN V+K AEQTP + L Sbjct: 166 MGEIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQTPASIL 225 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + +I + PPGV+NIV G+G AG A+A+ + + K+AFTGST +G I + + N+ Sbjct: 226 VLMEIIGDL-LPPGVLNIVNGYGIEAGQALATSKRIAKIAFTGSTPVGSHI-LKCAAENI 283 Query: 280 KRVTLELGGKSPNIIMSDA------DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYD 333 T+ELGGKSPNI SD +D VE A FFNQG+ C SR VQED+++ Sbjct: 284 IPSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLA-FFNQGEVCTCPSRALVQEDMFE 342 Query: 334 EFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG----- 388 EF+++ V R KS GNP D+ + G Q + QF KI+ Y+ GK+EGA +L GG Sbjct: 343 EFMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTGGDREHL 402 Query: 389 GIAADRGYFIQPTVF-GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 + G++IQPT+F GD + M + +EEIFGPV+ + FKT EE + AN++ +GL A Sbjct: 403 DEEFNNGFYIQPTLFKGD--NKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEFGLGAG 460 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506 V+T+D + A + + +QAG VW+NCY + A + FGGYK SG GRE + L+ Y + K Sbjct: 461 VWTRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHYQQTK 519 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: 689 Number of extensions: 34 Number of successful extensions: 7 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: 533 Length adjustment: 35 Effective length of query: 482 Effective length of database: 498 Effective search space: 240036 Effective search space used: 240036 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 Apr 09 2024. 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