Align succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized)
to candidate WP_011840207.1 RSPH17029_RS00810 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-20455 (480 letters) >NCBI__GCF_000015985.1:WP_011840207.1 Length = 486 Score = 291 bits (745), Expect = 3e-83 Identities = 169/475 (35%), Positives = 254/475 (53%), Gaps = 17/475 (3%) Query: 12 YINGEWLSALGGETQSIFNPATGQLIGTVPMMGRQEARQAIAAANQALPAWRALPAKERS 71 YING W + + +P+T + + + + + A+AAA A W A P ER Sbjct: 8 YINGGWTAPAKARDCEVIDPSTEEACAVISLGDQADTDAAVAAAKAAFEGWAATPPAERL 67 Query: 72 ARLRAWFELMLEHQEELARLMTIEQGKPLAEARNEIL-----YAASFVEWFAE-EGKRVY 125 ++ +EE+A+ +++E G P+ ARN + +F++ F E E R Sbjct: 68 RLVKGILAQYEARKEEMAQAISLEMGAPIDLARNSQAPCLPWHLTNFLKAFEEIEWVRPL 127 Query: 126 GDVIPSPQADKRLLVIKQPVGVTAAITPWNFPSAMITRKAAPALAAGCTMVLKPAPQTPF 185 G P+ + + +P+GV ITPWN+P +T K PAL AGCT VLKP+ + P Sbjct: 128 GPHAPNDR------IALEPIGVVGLITPWNWPMNQVTLKVIPALLAGCTCVLKPSEEAPL 181 Query: 186 SALALAALAQRAGIPAGVFNVVTGSAQEIGGEFTGNPIVRKLTFTGSTHIGRLLMAQCAH 245 S+L A AG+PAGVFN+V G +G + + +P V ++FTGST GR + A Sbjct: 182 SSLLFAEFVHDAGLPAGVFNLVNGDGAGVGTQLSSHPDVEMISFTGSTRAGRAISKAAAE 241 Query: 246 DVKKMSLELGGNAPFIVFEDADLDKAAEGALIAKYRNNGQTCVCTNRIYVHDSVHDAFAG 305 +K+++LELGG ++F DAD ++A E + + N+GQ+C R+ V +D Sbjct: 242 SLKRVTLELGGKGANLIFADAD-ERAVERGVKHCFNNSGQSCNAPTRMLVERPFYDRAVE 300 Query: 306 KLKKAVEGLRVGNGLEDGVTVGPLINDAAVQKVRSHIADAVGKGASILAG--GKPHALG- 362 + RV + E+G +GP++N ++++S+I + +GA ++AG G+P L Sbjct: 301 IAAEVAAKTRVASAHEEGPHIGPVVNKRQFEQIQSYIQKGIDEGARLVAGGLGRPDGLNR 360 Query: 363 GTFFEPTILANVPHDALVAHEETFGPLAPLFRFRDEAEVVGRANDTEYGLAAYFYTENLG 422 G F PT+ A+V + EE FGP+ + F E E V ANDT YGL Y +E+ Sbjct: 361 GFFVRPTVFADVTPGMTIEREEIFGPVLSILPFETEEEAVRIANDTPYGLTNYVQSEDGA 420 Query: 423 RIFRVAEALEYGMVGINCGAISNEVAPFGGVKASGLGREGSKYGIEEYLEIKYLS 477 R R+A L GMV +N G APFGGVKASG REG +GIEE+LE+K +S Sbjct: 421 RRNRLARRLRSGMVEMN-GKSRGAGAPFGGVKASGRAREGGVWGIEEFLEVKAIS 474 Lambda K H 0.319 0.135 0.399 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: 582 Number of extensions: 28 Number of successful extensions: 5 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: 480 Length of database: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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 Apr 10 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