Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 372 bits (954), Expect = e-107 Identities = 207/482 (42%), Positives = 290/482 (60%), Gaps = 18/482 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI +W V + F +P G+V CQVA D+ D++ A+ AA AA W + + Sbjct: 22 FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAA---KDAWGKTSVT 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R LL ++AD +E++ +LA ET +NGK + DL + + RY+AG G Sbjct: 79 ERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGS 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 ID + SY EP+GV GQIIPWNFPLLM AWK+ PALA GN +V+K AEQTP++ L Sbjct: 139 AADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPVSIL 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + LI++ P GV+NIV GFG AG A+A + + K+AFTGST+IG I A S L Sbjct: 199 VMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKCAAES-L 256 Query: 280 KRVTLELGGKSPNIIMSDA------DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYD 333 T+ELGGKSPNI +D +D AVE A FFNQG+ C SR + E IYD Sbjct: 257 IPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVLIAESIYD 315 Query: 334 EFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG---GI 390 +F+++ +ARAK+ GNP D+ T+ G Q + QF KIL Y+ G+ EGA++L GG + Sbjct: 316 KFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSCQL 375 Query: 391 AADR--GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAV 448 + D+ G++I+PT+ + M + +EEIFGPV+ + FK E + AN++ YGL A V Sbjct: 376 SGDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGV 434 Query: 449 FTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508 +T+D+++A + + +QAG VW+NCY + A + FGGYK SG GRE + L Y K + Sbjct: 435 WTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNL 494 Query: 509 TV 510 V Sbjct: 495 LV 496 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: 638 Number of extensions: 36 Number of successful extensions: 6 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: 506 Length adjustment: 35 Effective length of query: 482 Effective length of database: 471 Effective search space: 227022 Effective search space used: 227022 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