Align Putative succinate-semialdehyde dehydrogenase C1002.12c [NADP(+)]; SSDH; EC 1.2.1.16 (characterized)
to candidate Echvi_1497 Echvi_1497 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q9US47 (547 letters) >FitnessBrowser__Cola:Echvi_1497 Length = 469 Score = 166 bits (421), Expect = 1e-45 Identities = 106/343 (30%), Positives = 178/343 (51%), Gaps = 16/343 (4%) Query: 207 QPVGVVGIITPWNFPAAMITRKVGAALAAGCTVVIRPAAETPFTALALAKLAERAGVPAG 266 +P G V II+PWN+P + + +A+AAGC+ ++P+ +P T+ L ++ Sbjct: 101 EPKGAVLIISPWNYPFNLSVAPLVSAIAAGCSACLKPSEHSPHTSALLRRMVTE------ 154 Query: 267 VLNMVTANSPSEHGIELTTNPLIRK---VSFTGSTNVGKILAKQSSSTLKKLSLELGGNA 323 L V + E G+ +T+ L + + FTGST VGKI+ K ++ L ++LELGG + Sbjct: 155 -LFAVEDVTIFEGGVPVTSELLEQPFDHIFFTGSTEVGKIVMKAAAKNLTSVTLELGGKS 213 Query: 324 PFIVFEDADLEKAADALMACKFRGSGQTCVCANRIYVHSSVYDAFVDLVTERVSKF--KL 381 P I+ + DLE AA + KF SGQTC+ + ++VH S F++ + +V++ Sbjct: 214 PAIIDQGFDLEDAAKKIAIGKFINSGQTCIAPDYLFVHESQKQDFIETLKAQVNRMYNAN 273 Query: 382 GYGLDAGVTHGPLISEKAISKVKQHVEDAVQKGGVVVTGGKVASNLGPMYFEPTVIINAK 441 G G D +G +I I +++ ++DA KG V GGK ++L + EPTV+ N Sbjct: 274 GKGFDRNPDYGRIIHAPHIVRLQNMLKDAQTKGAHVEFGGK--NSLDQQFMEPTVVSNVS 331 Query: 442 QGMLISEEETFGPVGALFKFDTEDEVVAWANDSPVGLAGYLFSKDISRVFRVGEALQVGM 501 + M + +EE FGP+ + + D+V+ P LA Y F+ D + ++ + G Sbjct: 332 EAMDLMKEEIFGPILPIITYHQLDDVIQLIQLKPKPLAVYAFTTDDRIIEQLSKNTSSGA 391 Query: 502 VGCNTGLVSDVLS--PFGGVKESGFGREGSKYGISEYLDIKSL 542 + N + + S PFGG+ SG GR G + + K++ Sbjct: 392 LVINDCAIQFLHSELPFGGIGASGMGRSHGHAGFLAFSNEKAI 434 Lambda K H 0.317 0.133 0.380 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: 497 Number of extensions: 20 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: 547 Length of database: 469 Length adjustment: 34 Effective length of query: 513 Effective length of database: 435 Effective search space: 223155 Effective search space used: 223155 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 (21.6 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