Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 314 bits (805), Expect = 4e-90 Identities = 186/461 (40%), Positives = 253/461 (54%), Gaps = 3/461 (0%) Query: 12 IDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHL 71 IDG +V A +V NPA+G L++ V A E A+ AA A WA + A ER L Sbjct: 16 IDGQWVRGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWAARTAKERGAIL 75 Query: 72 RRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDRP 131 RR + I A A +AR +T EQGK + A+ EV + A ++D+ AE A+R G I + P Sbjct: 76 RRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKRAYGHTIPTPMP 135 Query: 132 GENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLV 191 G+ + ++P+GV A I PWNFP +I RK+ PAL G T+VVKP+ ETP + ARL Sbjct: 136 GKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSALAIARLA 195 Query: 192 AETDLPRGVFNVV--CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLE 249 E +P GV N+V + +VG L V +SFTGS G + A + KL+LE Sbjct: 196 TEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKKLSLE 255 Query: 250 LGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAA 309 LGG AP IV DADLE AV S+ N+GQ C CA R+ VQ + + F R+A +AA Sbjct: 256 LGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAARLAEKVAA 315 Query: 310 TRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLT 369 + G E V++GPLIN L K+ V A+ GA ++TGG + GH YQPTVL Sbjct: 316 LKVGPGTGE-GVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLGGHFYQPTVLV 374 Query: 370 GCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELD 429 G + RI +EEIFGPV PI + EA+ LAN +GL + ++RD+ + +++ Sbjct: 375 GATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRCWRVAEQIE 434 Query: 430 FGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHT 470 G IN GV++SG+G GL EY T Sbjct: 435 AGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLET 475 Lambda K H 0.320 0.136 0.395 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: 553 Number of extensions: 21 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: 477 Length of database: 485 Length adjustment: 34 Effective length of query: 443 Effective length of database: 451 Effective search space: 199793 Effective search space used: 199793 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 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