Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate 6937537 Sama_1693 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= CharProtDB::CH_007085 (453 letters) >FitnessBrowser__SB2B:6937537 Length = 867 Score = 311 bits (797), Expect = 5e-89 Identities = 168/439 (38%), Positives = 256/439 (58%), Gaps = 8/439 (1%) Query: 1 MSNEVSIKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVY 60 ++N + EL+ + AQ + +YSQEQVD + +A D AK A EET MGV Sbjct: 3 VTNTQELNELVARVAKAQAQFASYSQEQVDRIFRAAALAAADARIRLAKMAAEETRMGVV 62 Query: 61 EDKVAKCHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMC 120 EDKV K H S I+N KD+KT GI+ E+ + +A+P G++ P TNP T + Sbjct: 63 EDKVIKNHFASEYIYNKYKDEKTCGILAEDATFGTITIAEPVGIICGIVPTTNPTSTAIF 122 Query: 121 NAMAAIKGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELM 180 A+ ++K RN II +PHP+AK + ++ GAP++II ++ PS + +LM Sbjct: 123 KALISLKTRNGIIFSPHPRAKVSTTTAARIVLDAAIAAGAPKDIIGWIDEPSVALSNQLM 182 Query: 181 --ESADVVIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDN 238 E ++++ATGG G VKAAYSSG+PA GVG GN+ +++D+ D +A I+ + +DN Sbjct: 183 THEKINLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTFDN 242 Query: 239 GIICSSEQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSV 298 G++C+SEQ+V+ YD V F +G + + +E + + KDG +N+ I+G+S Sbjct: 243 GVVCASEQAVVVVDAVYDAVKERFSSHGGYLLSKKENA-ALQKVILKDGGLNADIVGQSA 301 Query: 299 QIIADLAGVKVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYM 358 IA +A +KVP TKV++ + EK+ EK+ P+L + FEEA++ A A Sbjct: 302 ATIAAMANIKVPAHTKVLIGEVTDIDEKEAFAHEKLSPLLGMYRAANFEEALDKAEALVA 361 Query: 359 YEGAGHTAGIHSD---NDENIRYAGTVLPISRLVVNQPATTA--GGSFNNGFNPTTTLGC 413 G GHT+G+++D DE ++ G + +R+++N PA+ G +N P+ TLGC Sbjct: 362 LGGIGHTSGLYTDQDTQDERVKSFGYRMKTARILINTPASQGGIGDLYNFKLAPSLTLGC 421 Query: 414 GSWGRNSISENLTYEHLIN 432 GSWG NSISEN+ HLIN Sbjct: 422 GSWGGNSISENVGPSHLIN 440 Lambda K H 0.313 0.131 0.368 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: 904 Number of extensions: 52 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: 453 Length of database: 867 Length adjustment: 37 Effective length of query: 416 Effective length of database: 830 Effective search space: 345280 Effective search space used: 345280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 54 (25.4 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