Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_041098592.1 SUTH_RS08615 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000828635.1:WP_041098592.1 Length = 480 Score = 326 bits (835), Expect = 1e-93 Identities = 189/450 (42%), Positives = 260/450 (57%), Gaps = 2/450 (0%) Query: 19 SAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKI 78 + A L++ NPA G + VP A E RA+ AA AA W K A ERA LRR + Sbjct: 21 TGATLDIRNPATGEAVGSVPGFGAAETRRAIDAAHAAFHPWRAKTAAERAKILRRWFELM 80 Query: 79 RADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASDRPGENIFLF 138 + +AR +T EQGK + A E+ + A ++++ AE ARR+ G++I S + + Sbjct: 81 MENQEDLARLMTQEQGKPLAEARGEIAYAASFIEWFAEEARRIYGDVIPSPLADRRLIVL 140 Query: 139 RKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPR 198 ++P+GV A I PWNFP +I RK+APAL G T+VVKP+E+TP + A L + LP Sbjct: 141 KQPVGVCAAITPWNFPAAMITRKVAPALAAGCTMVVKPAEQTPLSALALAWLGQQAGLPP 200 Query: 199 GVFNVVCGAG-QVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAI 257 GV NVV G +GG L+S+P V +SFTGS E G +M AP + K++LELGG AP I Sbjct: 201 GVLNVVTGEPVAIGGELTSNPKVLKLSFTGSTEIGRLLMGQCAPTIKKMSLELGGNAPFI 260 Query: 258 VLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRYGDPLA 317 V DADL+ AV S+ N+GQ C C R VQ V + F +R+AAA+A + G L Sbjct: 261 VFDDADLDAAVAGAMLSKYRNTGQTCVCTNRFLVQEGVHDAFAQRLAAAVAGLKVGYGL- 319 Query: 318 EPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRI 377 E V GPLI+ GL K++ + ALA+GA ++ GG + G ++PTVL G R+ Sbjct: 320 EEGVTQGPLIDGAGLAKVEELLADALAKGARVLCGGKRHAKGGTFFEPTVLAGATPAMRL 379 Query: 378 MREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINR 437 REEIFGPV PI D +AI +AND E+GL + F+RD+ +A LD+G IN Sbjct: 380 AREEIFGPVAPIFSFKDEADAIRMANDTEFGLAAYFFSRDIARAWRVGEALDYGMVGINS 439 Query: 438 EHFEAMQGFHAGVRKSGIGGADGKHGLYEY 467 GV++SG+G K+G+ EY Sbjct: 440 GMISNEVAPFGGVKQSGLGREGSKYGIEEY 469 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: 524 Number of extensions: 21 Number of successful extensions: 4 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: 480 Length adjustment: 34 Effective length of query: 443 Effective length of database: 446 Effective search space: 197578 Effective search space used: 197578 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 Apr 09 2024. 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