Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_010961010.1 MCA_RS08650 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000008325.1:WP_010961010.1 Length = 491 Score = 317 bits (812), Expect = 6e-91 Identities = 190/463 (41%), Positives = 259/463 (55%), Gaps = 6/463 (1%) Query: 9 RNYIDGAFVESAAHLEVFN---PANGALLSRVPAASAEEVERALAAARAAQKDWARKPAI 65 R IDG +V+ A H + F+ PA G L+ VPA A E RA+AAA A W K A Sbjct: 16 RCLIDGQWVD-ADHSKTFSVTDPATGRALADVPAMGAAETMRAIAAAEHAWTGWRGKTAK 74 Query: 66 ERAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEI 125 ERA LRR I + +AR +T EQGK + A E+ + A ++++ AE A R GE Sbjct: 75 ERAAVLRRWYELILSHTEDLARILTAEQGKPLTEARNEIGYAAGFVEWFAEEAGRAYGET 134 Query: 126 IASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCF 185 I S P + + + R+P+GV A I PWNFP +I RK+APAL G T+VVKP+E+TP Sbjct: 135 IPSPVPDKRLLVIRQPIGVCAAITPWNFPAAMITRKIAPALAAGCTVVVKPAEQTPLTAL 194 Query: 186 EFARLVAETDLPRGVFNVVCGAGQ-VGGALSSHPGVDLISFTGSVETGARIMAAAAPNLT 244 A L + P GV NVV G + +GG L+S+P + +SFTGS E G +MA A + Sbjct: 195 ALADLAVQAGFPPGVINVVTGDPEAIGGELTSNPLIRKLSFTGSTEVGRLLMAQCAATVK 254 Query: 245 KLNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIA 304 K++LELGG AP IV DADL+ AV+ S+ N+GQ C C R +Q + + F ER+A Sbjct: 255 KISLELGGNAPFIVFEDADLDAAVEGALLSKYRNTGQTCVCTNRFLIQDSIYDAFAERLA 314 Query: 305 AAMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQ 364 A + G+ L E V+ GPLI+ L K++ + AL +GA ++ GG G +Q Sbjct: 315 AKVRRLEVGNGLDEGVVQ-GPLIDEQALAKVERHIADALDRGARVLAGGGRHPLGGRFFQ 373 Query: 365 PTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHA 424 PTVL + REE FGPV P+ +EA+A+AN EYGL + +TRDL +A Sbjct: 374 PTVLVDVTPEMLCTREETFGPVAPLLRFGSEEEALAIANATEYGLAAYFYTRDLARAFRV 433 Query: 425 LRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEY 467 L++G IN GV++SGIG HG+ EY Sbjct: 434 GEALEYGMVGINTGMLSYDVAPFGGVKQSGIGREGSHHGMDEY 476 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: 557 Number of extensions: 20 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: 491 Length adjustment: 34 Effective length of query: 443 Effective length of database: 457 Effective search space: 202451 Effective search space used: 202451 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 24 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