Align Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (characterized)
to candidate WP_012468985.1 GLOV_RS04485 aldehyde dehydrogenase
Query= SwissProt::P94428 (462 letters) >NCBI__GCF_000020385.1:WP_012468985.1 Length = 483 Score = 294 bits (752), Expect = 5e-84 Identities = 168/458 (36%), Positives = 265/458 (57%), Gaps = 13/458 (2%) Query: 8 YNPATGEEIKTIPQQSATEVEEAIERSHQAFKTWSKTSANERTSLLKKWYELIVEHKEEL 67 +NP TGE + T+ S + A+ + AF W+ + +++ L K +L+ + K+EL Sbjct: 25 FNPYTGEILTTVANGSQQDALLAVNAAADAFPDWAAVAPSQKRLLFLKAADLLEKRKDEL 84 Query: 68 ADLITKENGKPYQEAVGEVLYGAGYIEWFAEEAKRVYGRTVPAPTTGKRIVVTRQPVGPV 127 DL+ +E G A + G Y+ +A RV G +P+ TT K +V R PVG V Sbjct: 85 IDLLARETGAARPFAAYQAAAGPNYLREAGSQAHRVTGTILPSETT-KVSMVMRHPVGVV 143 Query: 128 AAITPWNFPNAMITRKAAPALAAGCTFIIKPAPDTPLSA-YELARLAYEAGIPKDVLQVV 186 A I+PWN P + R A+A G T ++KP+ ++P+S LA L EAG PK V +V Sbjct: 144 AGISPWNCPVVLSLRAVCFAMAYGNTVVLKPSEESPVSGGILLAELFEEAGFPKGVFNIV 203 Query: 187 I---GDGEEIGNVFTSSPKIRKITFTGSTPVGKILMKNSADTVKHVSMELGGHAPLIVDE 243 G E+G++F ++++I+FTGST VG+ L + +K +++ELGG+ PLIV Sbjct: 204 THGYGRSSEVGDLFIQDRRVKRISFTGSTRVGRELAEKCGRHLKRIALELGGNDPLIVLN 263 Query: 244 DADIDLAVEQAMASKYRNAGQTCVCANRLIVHESIKDEFAAKLSEQVSKLKVGNGLEEGV 303 DAD+D AV A+ ++ + GQ C+ A RLI+ +++ EF A+ + S LKVGN L+ Sbjct: 264 DADMDHAVNAAIFGRFLHQGQVCMNAKRLIIEKTVAQEFTARFVARTSALKVGNPLDAAT 323 Query: 304 NVGPIINKRGFEKIVSQIDDAVEKGAKVIAGGTYDRNDDKGCYFVNPTVLTDVDTSMNIM 363 +GP+IN + +E + Q++ AV +GA+++ GG + CY +PTVL +V M+I Sbjct: 324 VIGPLINHKQYETLEGQVNRAVAEGAELLCGG----YGNGLCY--HPTVLGNVREDMSIF 377 Query: 364 HEETFGPVAPIVTFSDIDEAIQLANDTPYGLAAYFFTENYRRGIYISENLEYGIIGWNDG 423 HEETFGPVAPI+ D D+A++LAN + YGL+A T N ++G+ ++ +E G ND Sbjct: 378 HEETFGPVAPIIVAEDADDALRLANSSAYGLSAGILTNNMQQGLALARRIESGACHVNDS 437 Query: 424 G-PSAVQAPFGGMKESGIGREGGSEGIEPYLETKYLSI 460 AP GG+ SG G+ G E + + E +++++ Sbjct: 438 PLYGETHAPLGGVNNSGWGK-FGIEAMHEFTEQQWVTL 474 Lambda K H 0.314 0.134 0.388 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: 555 Number of extensions: 23 Number of successful extensions: 7 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: 462 Length of database: 483 Length adjustment: 33 Effective length of query: 429 Effective length of database: 450 Effective search space: 193050 Effective search space used: 193050 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: 42 (21.9 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