Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__ANA3:7023012 Length = 506 Score = 242 bits (618), Expect = 2e-68 Identities = 151/481 (31%), Positives = 249/481 (51%), Gaps = 27/481 (5%) Query: 14 QFVTWRGDAWIDVVN--------PATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPA 65 ++ + G W+ VN P +IP D A+DAA A+ W Sbjct: 18 KYANFIGGKWVAPVNGDYFENRSPVNGQNFCKIPRSDYRDIELALDAAHAAKDAWGKTSV 77 Query: 66 IERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEG 124 ERA+ L +I+ + + ++ E GK +++ ++ D+ Y A R EG Sbjct: 78 TERANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137 Query: 125 EIIQSDRPGENILL-FKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183 D G + F LGV I+PWNFP + A K+APAL GN +V+KP+E TP Sbjct: 138 SAADID--GNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPV 195 Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243 + + ++++++ LP G+ N+V G G GQ LA + ++A ++ TGS G I+ AA+ Sbjct: 196 SILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKCAAE 254 Query: 244 NITKVCLELGGKAP----AIVMDDAD--LELAVKAIVDSRVINSGQVCNCAERVYVQKGI 297 ++ +ELGGK+P A VMD D L+ AV+ ++ + N G+VC C RV +Q+ I Sbjct: 255 SLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVLIQESI 313 Query: 298 YDQFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKA 357 YD+F+ ++ Q ++ GNP + +G + +++ +A +EGA+V GG Sbjct: 314 YDRFIEKVLARAQTIKQGNPLD-TATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSL 372 Query: 358 VE-----GKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLT 412 + KGYY PT++ +M I EE FGPV+ V F +A+++AND++YGL Sbjct: 373 CQLEGDQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLG 431 Query: 413 SSIYTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQT 472 + ++T+++N A + +G++ G +IN + G++KSGIG K L+ Y T Sbjct: 432 AGVWTRDMNRAQRLGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNT 491 Query: 473 Q 473 + Sbjct: 492 K 492 Lambda K H 0.318 0.135 0.392 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: 571 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 479 Length of database: 506 Length adjustment: 34 Effective length of query: 445 Effective length of database: 472 Effective search space: 210040 Effective search space used: 210040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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