Align Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (uncharacterized)
to candidate 8501044 DvMF_1780 Aldehyde Dehydrogenase (RefSeq)
Query= curated2:O32507 (477 letters) >FitnessBrowser__Miya:8501044 Length = 560 Score = 148 bits (373), Expect = 5e-40 Identities = 138/461 (29%), Positives = 192/461 (41%), Gaps = 24/461 (5%) Query: 21 YTGETVKTFPFLESAEIPALIERADQAYRE----WGQRPVTERAAIMRRAAELMLERTDE 76 +T + P L+ A ++ AD A+ + W V ER + A M R E Sbjct: 80 FTPRLLGRCPILDEAAALRAVDAADHAWADGMGAWPTMGVAERIRHVEDFARRMAARRTE 139 Query: 77 LASLITLEMGKLLREAKGE-------VALAASILNYYGEQGPSFLEPKTIPVPQGEAAVL 129 + ++ E+ K ++A GE + L F+ K I A + Sbjct: 140 VVRIMMWEICKSWQDASGEFDRTMEYLRDTIDALKDLDRASSRFVIEKGI-----YAQIR 194 Query: 130 HAPLGVLLGIEPWNYPLYQVVRFAAPNLVVGNTVLLKHSELCPQSALALEQLFHDAGVPQ 189 APLG +L + P+NYPL + P L++GN V++K L L + F DA P Sbjct: 195 RAPLGPVLCMGPYNYPLNETFCTLMPALIMGNPVIVKTPRLGRLLYSPLMEAFRDA-FPA 253 Query: 190 GAYTNLFLRIADIEQVIAHPAVQGVSLTGSERAGASVAELAGR--HLKKCVLELGGSDPF 247 G L ++ ++A + ++ GS A A LA H +CVL L + Sbjct: 254 GVVNILHGDRRIVKPIMASGRINVLAFIGSSTA-ADALRLAHPYPHRLRCVLGLDAKNAG 312 Query: 248 IVLDAEDLDTTVKAAATGRLSNTGQACIAAKRLMVVDDLYDEFVSRLGQTFSAFVPGDPA 307 IVLD D+D TV A G S GQ C A K L V DEF++R+ + G P Sbjct: 313 IVLDCADMDLTVAEALQGSFSFNGQRCTALKMLFVHQKRLDEFLARMDEGIRKLRIGMPW 372 Query: 308 DPSTRLGPLSSEQAARDLQAQVQDAIDKGATVVAGGQRPEHPGAFVQPTVLTDVTPDMRA 367 D R+ PL + L VQDA +G V G H PTV+ TP MR Sbjct: 373 DEGVRITPLPVPGKSAYLDDLVQDAAAQGGKVANSG-GGTHAETLYHPTVVCPATPQMRV 431 Query: 368 YHEELFGPVAVVYRVRDEDEAVALANASTYGLGGAVFSSDLDRAQRVAERL--DTGMVWI 425 YHEE FGPV V D + V S YG ++F +D D R+ + + V I Sbjct: 432 YHEEQFGPVIPVIPFTDIETPVRYVVGSQYGQQLSIFGNDPDDVARLIDPMVNQVCRVNI 491 Query: 426 NHPTSSAAD-LPFGGVKRSGFGRELSSMGMLEFTNQKLVRA 465 N D PF G K S G S + F+ + LV A Sbjct: 492 NSQCQRGPDTFPFTGRKDSAEGTLSVSDALRCFSIRTLVAA 532 Lambda K H 0.317 0.133 0.384 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: 623 Number of extensions: 26 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: 560 Length adjustment: 35 Effective length of query: 442 Effective length of database: 525 Effective search space: 232050 Effective search space used: 232050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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