Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_090273153.1 BLU11_RS09735 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_900105005.1:WP_090273153.1 Length = 493 Score = 424 bits (1091), Expect = e-123 Identities = 211/444 (47%), Positives = 300/444 (67%) Query: 2 LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61 +ATL S + E A+ + A A WA+T PR R++ L A+ ++ A E A +++ EM Sbjct: 45 IATLPSLSPEQAIEEVAIAYQAGRDWAKTTPRHRSDTLHNAYLVLIANKERLAYVISREM 104 Query: 62 GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121 GK LAEA+GEV Y A+++RW+++E +R G Y P G + IL + PVG LLI PWNF Sbjct: 105 GKTLAEAQGEVQYAADYVRWYADELLRPAGGYRDNPAGGSTILTKRAPVGLALLIAPWNF 164 Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181 P+AM TRK+APA+AAGC V+KPA LTPLT+ L + EAG+P ++ VV+++ +S S Sbjct: 165 PMAMITRKIAPAIAAGCASVIKPAGLTPLTTLLTVDLLAEAGVPRELMRVVTTTQSSAFS 224 Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241 +L D R+RK+SFTGST VG LM A+++++++SMELGGNAP +VF+DADL++AVEGA Sbjct: 225 EAVLADPRVRKISFTGSTSVGSTLMGLAAQNIVKSSMELGGNAPLIVFDDADLERAVEGA 284 Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301 + AK+RN G++C AANR VQ+ +A +F F+ M + G +GP+IN A Sbjct: 285 ILAKLRNGGQSCVAANRIYVQDGIASDFVEAFSKRMSQMVLGHSIAEGVDLGPVINRDAV 344 Query: 302 DDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTTF 361 ++ LV AV GA TGG +G GYF++ TVL VP +A I EIFGP+A ++ F Sbjct: 345 NNFQRLVDDAVTRGAELRTGGRAPEGAGYFFEATVLDRVPLDADIANTEIFGPIAAISRF 404 Query: 362 TTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVKQ 421 +T+++ I+ AN + +GLA Y+++ + +R L VA+Q+E G+VG N G+ SN AAPFGG+KQ Sbjct: 405 STQEEVIQRANDTPFGLAGYVFTENLDRALNVADQLETGLVGINNGVPSNPAAPFGGMKQ 464 Query: 422 SGLGREGGSEGIAEYTTTQYIGIA 445 SGLGREG EG+ EY +Y IA Sbjct: 465 SGLGREGSHEGLEEYQEIRYYNIA 488 Lambda K H 0.317 0.131 0.376 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: 512 Number of extensions: 16 Number of successful extensions: 1 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: 450 Length of database: 493 Length adjustment: 33 Effective length of query: 417 Effective length of database: 460 Effective search space: 191820 Effective search space used: 191820 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: 51 (24.3 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