Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__Cup4G11:RR42_RS24555 Length = 494 Score = 620 bits (1598), Expect = 0.0 Identities = 304/480 (63%), Positives = 373/480 (77%) Query: 3 LNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP 62 L DPSLL + ++ W +A+ + A+TNPATG ++A V + AE ++AI A+ A Sbjct: 15 LRDPSLLETRAWLASGWQEASGGRSFAVTNPATGEILARVASLSGAEVESAITASAQAQA 74 Query: 63 AWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEE 122 W+ ++ ER LR WF+L+ N+DDLAL+MTSEQGKPL EA+GE+ YAASF+EWFAEE Sbjct: 75 VWQRRSSHERAKLLRAWFDLMIANADDLALIMTSEQGKPLAEARGEILYAASFVEWFAEE 134 Query: 123 AKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPA 182 AKRIYGD P Q DKRI+VI+QPVGV AAITPWNFPAAMITRK APALAAGC+++V+PA Sbjct: 135 AKRIYGDVAPHPQTDKRILVIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRPA 194 Query: 183 PQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLM 242 TP TALALAVLAERAGIPAGV ++ G + IG + +P+VRKLSFTGST VG LM Sbjct: 195 DLTPLTALALAVLAERAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVLM 254 Query: 243 AQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVY 302 +Q +PT+K+LSLELGGNAPFIVFDDA++DAA+EGAM +KYRN+GQTCVCANR VQ G+Y Sbjct: 255 SQSSPTIKRLSLELGGNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDGIY 314 Query: 303 DEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHE 362 D F E L VA+LKVG G+ GV GPLI +A E +Q+ ++DA+ KGA V+ GGK H Sbjct: 315 DRFVEALVRRVAELKVGNGVEPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGHA 374 Query: 363 LGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRD 422 LGG FFEPTV+ A MRVAREE FGP+AP+F+F D + I ANDTE+GLAAY Y RD Sbjct: 375 LGGTFFEPTVIAGATPDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTRD 434 Query: 423 ISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICMSV 482 + +W+V E+LEYGMVG+NTGLIS EVAPFGG+K SGLGREGS+YGI+EYLEIKY+C V Sbjct: 435 NARIWRVGEALEYGMVGLNTGLISNEVAPFGGVKQSGLGREGSRYGIDEYLEIKYLCAQV 494 Lambda K H 0.318 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: 702 Number of extensions: 22 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: 482 Length of database: 494 Length adjustment: 34 Effective length of query: 448 Effective length of database: 460 Effective search space: 206080 Effective search space used: 206080 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