Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011777430.1 MVAN_RS00555 aldehyde dehydrogenase family protein
Query= BRENDA::P47740 (484 letters) >NCBI__GCF_000015305.1:WP_011777430.1 Length = 470 Score = 396 bits (1017), Expect = e-114 Identities = 200/444 (45%), Positives = 292/444 (65%), Gaps = 9/444 (2%) Query: 5 VLRLRQAFRSGRSRPLRFRLQQLEALRRMVQEREKEILAAIAADLSKSELNAYSHEVITI 64 V +LRQ F +GR+R +++R +QL AL R++ E E I A+ DL + A+ +V + Sbjct: 23 VRKLRQTFATGRTRSVQWRKEQLHALERLMTENEGAIAEALEKDLGRGPFEAWLADVAST 82 Query: 65 LGEIDFMLGNLPELASARPAKKNLLTMMDEAYVQPEPLGVVLIIGAWNYPFVLTMQPLVG 124 +GE + N+ + R + + +V+ EP G VLIIGAWN+PF LT+ P VG Sbjct: 83 VGEAAYAAKNVGKWMKRRYRLLEMSQLPGRGWVEYEPYGTVLIIGAWNFPFALTLGPAVG 142 Query: 125 AIAAGNAAIVKPSELSENTAKILAELLPQYLDQDLYAIVNGGIPETTELLKQRFDHILYT 184 AIAAGN ++KPSE++ ++ ++AEL+P+Y+D D A+V G + EL+ Q FDH+++T Sbjct: 143 AIAAGNTVVLKPSEVAPASSALMAELVPRYMDNDAIAVVEGDGAVSQELIAQGFDHLIFT 202 Query: 185 GNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDRDCDLDVACRRIAWGKYMNCGQTCIAP 244 G T VG+ V EAAA HLTPVTLELGGKSP + D D++VA +RIAW K +N GQ CIAP Sbjct: 203 GGTEVGRRVYEAAATHLTPVTLELGGKSPVIVAADADIEVAAKRIAWTKLINSGQICIAP 262 Query: 245 DYILCEASLQNQIVQKIKETVKDFYGENIKASPDYERIINLRHFKRLQSLL---KGQKIA 301 DY+L EA +++++V+ I++ + F N ++I+N RHF RL + L KG K+A Sbjct: 263 DYVLAEAPIRDKLVEAIRKAIDTFEAGNAAG----KKIVNERHFNRLANALAATKG-KVA 317 Query: 302 FGGEMDEATRYLAPTILTDVDPNSKVMQEEIFGPILPIVSVKNVDEAINFINDREKPLAL 361 GG D + PT++ D DP +M +EIFGPILP+V+V+N+DEAI+F+N R KPLA Sbjct: 318 IGGGSDAVAMKIQPTVVVDPDPAEPLMTDEIFGPILPVVTVQNLDEAISFVNSRPKPLAA 377 Query: 362 YVFSRNNKLIKRVIDETSSGGVTGNDVIMHFTVNSLPFGGVGASGMGAYHGKYSFDTFSH 421 Y+F++ + +RVI E +GG+ N +I HF + LPFGGVG SG+GAYHGK+ F+ FSH Sbjct: 378 YLFTKAKAVRERVIKEVPAGGMVVNHLIFHFATHKLPFGGVGPSGLGAYHGKFGFEEFSH 437 Query: 422 QRPCLLKGLKGESVNKLRYPPNSE 445 ++ L K + + + + YPP +E Sbjct: 438 RKSVLTKPTRPD-LGAMIYPPYTE 460 Lambda K H 0.321 0.138 0.400 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: 562 Number of extensions: 23 Number of successful extensions: 3 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: 484 Length of database: 470 Length adjustment: 33 Effective length of query: 451 Effective length of database: 437 Effective search space: 197087 Effective search space used: 197087 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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