Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_013834856.1 THICY_RS01540 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16246 (477 letters) >NCBI__GCF_000214825.1:WP_013834856.1 Length = 456 Score = 226 bits (575), Expect = 2e-63 Identities = 152/458 (33%), Positives = 238/458 (51%), Gaps = 8/458 (1%) Query: 23 LEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAGHLRRIAAKI-RAD 81 L+ NPA G L+ A E ++ A+ A A +W+++ ++ L + A KI RA Sbjct: 3 LQSINPATGEKLAEFEAWDQERLDLAIRRANAEFLEWSQRTSLATRCELIKNAGKILRAQ 62 Query: 82 AGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARR-LEGEIIASDRPGENIFLFRK 140 +A+ ITLE GK + A+ E+ +A D+ AE + L E IA+D ++ + Sbjct: 63 QDELAKLITLEMGKSINEAKAEIEKSAWVCDFYAEHGPKFLADEPIATD--ASKSYICYQ 120 Query: 141 PLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFARLVAETDLPRGV 200 PLG+V ++PWNFPF+ + R APAL+ GN ++K + P R+ E LP V Sbjct: 121 PLGLVLAVMPWNFPFWQVFRFAAPALIAGNIGLLKHASNVPQCAQAIERIFIEAGLPASV 180 Query: 201 F-NVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNLELGGKAPAIVL 259 F N++ G+ +V + S V ++ TGS G ++ A A L K LELGG IV+ Sbjct: 181 FTNLMIGSDKVESVIRSRY-VRAVTLTGSEPAGRKVAAIAGEELKKTVLELGGSDAFIVM 239 Query: 260 ADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMAATRY-GDPLAE 318 +DAD+ AV+A SR +N GQ C A+R V + E FI R+ A+ + GDPL + Sbjct: 240 SDADIPAAVEAAVTSRYLNMGQSCIAAKRFIVDTFIYEDFITRLKTAVESRFVEGDPL-D 298 Query: 319 PEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVLTGCRADTRIM 378 P + P+ + L+++ +V+T + GA LVTGG +RPG +Y PT+L + Sbjct: 299 PATTLCPMARQDLLDELHQQVQTCVDYGARLVTGGYQLDRPGCYYAPTILADISSAMPAY 358 Query: 379 REEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALRELDFGETYINRE 438 EE FGPV I + A+ LAN ++GL SV++ D A ++ G ++N Sbjct: 359 HEEFFGPVALIFKASEPAHAVGLANATQFGLGGSVWSSDGATAETMALRMESGACFVNGM 418 Query: 439 HFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476 + GV+ SG G HG+ E+T+ ++++ Sbjct: 419 TKSDPRLPFGGVKNSGYGRELSYHGIREFTNIKSIWIK 456 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: 439 Number of extensions: 25 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: 456 Length adjustment: 33 Effective length of query: 444 Effective length of database: 423 Effective search space: 187812 Effective search space used: 187812 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 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