Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)
Query= metacyc::MONOMER-16246 (477 letters) >FitnessBrowser__Burk376:H281DRAFT_03540 Length = 479 Score = 311 bits (797), Expect = 3e-89 Identities = 185/460 (40%), Positives = 253/460 (55%), Gaps = 2/460 (0%) Query: 10 NYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIERAG 69 +YI G + E A+ V NPA G ++++V A E +A+AAA A W A ER+ Sbjct: 9 HYIGGEWYEGASTYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRSLTAKERSA 68 Query: 70 HLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIASD 129 ++R + +A +T EQGK + A EV + A + ++ AE A+R G++I S Sbjct: 69 RVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSP 128 Query: 130 RPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEFAR 189 P I + R+P+GVVA I PWNFP +I RK PAL G T+V+KPSEETP + A Sbjct: 129 NPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSALALAV 188 Query: 190 LVAETDLPRGVFNVVCG-AGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKLNL 248 L + +P GVFNVV G A +GGAL+ V +SFTGS G + +A L KL+L Sbjct: 189 LAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSL 248 Query: 249 ELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAAMA 308 ELGG AP IV DADL+ AV+ S+ N+GQ C C R YVQ + + F +A A Sbjct: 249 ELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTLALAQAAR 308 Query: 309 ATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERPGHHYQPTVL 368 R G+ L + +VE GPLIN+ L K++A V AL +GA ++TG G Y+PTVL Sbjct: 309 KMRVGNAL-QGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGTFYEPTVL 367 Query: 369 TGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHALREL 428 + I +EE FGPV DEA+A AN +GL++ +TRDL +A L Sbjct: 368 VDASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARAWRVGEAL 427 Query: 429 DFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYT 468 + G IN GV++SG+G K+GL EYT Sbjct: 428 ESGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEYT 467 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: 527 Number of extensions: 23 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: 479 Length adjustment: 34 Effective length of query: 443 Effective length of database: 445 Effective search space: 197135 Effective search space used: 197135 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