Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 325 bits (832), Expect = 3e-93 Identities = 187/470 (39%), Positives = 269/470 (57%), Gaps = 4/470 (0%) Query: 5 VQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALP 64 V+ IDGQ+V RG+A DV+NPA +I+ + D A + AIDAA RA P W A Sbjct: 10 VETAALIDGQWV--RGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAART 67 Query: 65 AIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEG 124 A ER + LR+ S I A +++ L+ +E GK A+ EV + A +ID+ AE A+R G Sbjct: 68 AKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYG 127 Query: 125 EIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNN 184 I + PG+ + K+ +GV I PWNFP +I RK+ PAL G T+V+KP+ TP + Sbjct: 128 HTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLS 187 Query: 185 AIAFAKIVDEIGLPRGVFNLV-LGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243 A+A A++ E G+P GV N+V R VG+ L + +V +S TGS G+ + A Sbjct: 188 ALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAG 247 Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303 + K+ LELGG AP IV DDADLE AV + S+ N+GQ C CA R+ VQ GI+D F Sbjct: 248 TMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAA 307 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY 363 RL E + A++ G P + +GPLIN AL +V V+ AV+ GA V GG G+ Sbjct: 308 RLAEKVAALKVG-PGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLGGH 366 Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423 +Y PT+L+ EM I EE FGPV P+V F+T +A+ +AN + +GL + Y++++ Sbjct: 367 FYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRC 426 Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 + + ++ G IN G ++SG+G GL EYL+T+ Sbjct: 427 WRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETK 476 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: 531 Number of extensions: 25 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: 479 Length of database: 485 Length adjustment: 34 Effective length of query: 445 Effective length of database: 451 Effective search space: 200695 Effective search space used: 200695 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