Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 308 bits (788), Expect = 4e-88 Identities = 181/469 (38%), Positives = 257/469 (54%), Gaps = 5/469 (1%) Query: 11 YIDGAFVE--SAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERA 68 Y GA+ + S A V NPA G +++ VP E RA+AAA AAQK WA + A +RA Sbjct: 23 YFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRA 82 Query: 69 GHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIAS 128 LRR I +A +AR +T E GK + A EV + A ++++ AE A+RL GE I Sbjct: 83 QVLRRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEEAKRLYGETIPG 142 Query: 129 DRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFA 188 P I + R+P+GVV I PWNFP +I RK APAL G + KP+E+TP + A Sbjct: 143 HLPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALA 202 Query: 189 RLVAETDLPRGVFNVV--CGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246 L +P G+F V+ + +G + V ++FTGS + G ++A AA + K Sbjct: 203 VLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKC 262 Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306 ++ELGG AP IV DADL+ AV+ + N+GQ C CA R+YVQ V + F E++AAA Sbjct: 263 SMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAA 322 Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPT 366 + + GD AE V +GPLIN +EK+ + A+G T+VTGG G + PT Sbjct: 323 VEELKVGDGAAE-GVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTPT 381 Query: 367 VLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALR 426 V+TG + ++ REE FGPV P+ + DE IA+AND +GL + RD+ + Sbjct: 382 VVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSE 441 Query: 427 ELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYL 475 L++G IN GV++SG+G +HG+ EY + L Sbjct: 442 ALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICL 490 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: 563 Number of extensions: 22 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: 492 Length adjustment: 34 Effective length of query: 443 Effective length of database: 458 Effective search space: 202894 Effective search space used: 202894 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