Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate WP_084544763.1 H566_RS0105030 betaine-aldehyde dehydrogenase
Query= BRENDA::Q0K2K1 (483 letters) >NCBI__GCF_000482785.1:WP_084544763.1 Length = 525 Score = 310 bits (793), Expect = 1e-88 Identities = 188/473 (39%), Positives = 256/473 (54%), Gaps = 8/473 (1%) Query: 15 IDGEWTGAQSGAELAVCNPATGERIGSVPLAGAAEAEQAVRAAERALPAWRAQTGKARAA 74 I G + + SG NPATG + V +A E E A+ AA AW A TG R Sbjct: 48 IGGGYRASVSGECFEKLNPATGAPLCQVEIALEPEVEAAIAAAREGQRAWAALTGAERGR 107 Query: 75 VLRRWADLMLAHQEDLARLMTAEQGKPLPEARG-EVAYAASFLEWFGEEAKRVDGEVLAS 133 VL R L+ A ++LARL + GKPL EA +VA A LE+F A + G+ Sbjct: 108 VLMRAVALLRARNDELARLEVLDTGKPLQEAIAVDVASGADCLEYFAGMAATLRGDQY-- 165 Query: 134 PRSSQKMLVLREPVGVCAAITPWNFPAAMITRKVGPALAAGCTIIVKPAEQTPLTALALA 193 P + REP+G+C I WN+P + K PALA G +I KP+E TP TA LA Sbjct: 166 PLRNAFAYTRREPLGICVGIGAWNYPIQIALWKSAPALACGNAMIFKPSEMTPNTAAKLA 225 Query: 194 VLGEQAGVPRGVLQVVTGDAVQIGGVLCASPVVRKLSFTGSTAIGKLLMAQCAGTVKKLS 253 + +AGVP GV QV+ GD + G +L P V K+S TGS GK +MA A T+K+++ Sbjct: 226 EIYLEAGVPAGVFQVLQGDG-RTGRLLSTHPAVAKVSVTGSVPTGKRVMAAAADTLKRVT 284 Query: 254 LELGGNAPLIIFDDADLDRAVEGILASKFRNSGQTCVCANRIYVHDRVYDEVARRLVSAV 313 +ELGG + LI+FDDAD+++AV L + F G+ C R++VH+ V+D +R+V Sbjct: 285 MELGGKSALIVFDDADIEQAVTAALLANFYTQGEICTNGTRVFVHEAVHDRFVQRVVERA 344 Query: 314 EQLRPGHGVDSGVTQGPLIDADAVAKVEAHIADALAQGATVLTGGQR----HALGGTFFA 369 +L+ G +D G LI D AKV +I A+GA + GG R G F Sbjct: 345 GRLKLGDPLDMATQVGALISRDHAAKVLGYIDKGKAEGAECVLGGGRPDDAALAAGNFVL 404 Query: 370 PTVLANATASMRVAREETFGPLAPLFRFTSEAEVVAMANDTESGLAAYFFSRDMAKIWRV 429 PTV T M + +EE FGP+ + F+ E EVVA AN T GLA F+RD+A+ RV Sbjct: 405 PTVFTGCTDDMTIVKEEIFGPVMSVLTFSGEEEVVARANATPFGLAGGVFTRDIARGHRV 464 Query: 430 AQGLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSRHGIDEYLETKYLCMEV 482 A L+ G+ IN I+ PFGG K+SG+G E S I+ Y K + +E+ Sbjct: 465 AGQLDAGVCWINNYNITPIEMPFGGTKESGIGSENSHAAIEHYTRIKSVYVEL 517 Lambda K H 0.319 0.133 0.390 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: 610 Number of extensions: 34 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: 483 Length of database: 525 Length adjustment: 34 Effective length of query: 449 Effective length of database: 491 Effective search space: 220459 Effective search space used: 220459 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