Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Cup4G11:RR42_RS24555 Length = 494 Score = 221 bits (563), Expect = 4e-62 Identities = 163/466 (34%), Positives = 234/466 (50%), Gaps = 29/466 (6%) Query: 13 WVDGDAAR-FAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQAVVER 71 W + R FA T+P +GE L + S +VE A+ A+ QA W RRS ER ++ Sbjct: 31 WQEASGGRSFAVTNPATGEILARVASLSGAEVESAITASAQAQAVWQRRSSHERAKLLRA 90 Query: 72 FRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGERARDI---- 127 + + + + + LA + E GKPL EAR E+ + ++ E E A+ I Sbjct: 91 WFDLMIANADDLALIMTSEQGKPLAEARGEI--------LYAASFVEWFAEEAKRIYGDV 142 Query: 128 -----GDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTAD 182 D R ++ +P GV A P+NFP + + PAL AG +++ +P++ TP+TA Sbjct: 143 APHPQTDKRILVIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRPADLTPLTAL 202 Query: 183 LTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVD 241 AG+PAGV+ +V G + E+G L S + L FTGS +VG +L Q + Sbjct: 203 ALAVLAERAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVLMSQSSPTI- 261 Query: 242 KILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDA 301 K L+LELGGN P +V D D +AA+ + S + + GQ C CA R +V G + D ++A Sbjct: 262 KRLSLELGGNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDG-IYDRFVEA 320 Query: 302 LTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSL 361 L +AEL+V EP L A + L A DD V +G + + + G + Sbjct: 321 LVRRVAELKVGNGV-EPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGHALGGTF 379 Query: 362 LSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERADWD 419 P +I D V EE FGP+ V R+RD EAIALANDT YGL+A L + A Sbjct: 380 FEPTVIAGATPDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTRDNARIW 439 Query: 420 DFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSAYYAAD 463 + G+V N TG S+ APFGG+ SG R + Y D Sbjct: 440 RVGEALEYGMVGLN---TGLISNEVAPFGGVKQSGLGREGSRYGID 482 Lambda K H 0.319 0.135 0.409 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: 628 Number of extensions: 32 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: 489 Length of database: 494 Length adjustment: 34 Effective length of query: 455 Effective length of database: 460 Effective search space: 209300 Effective search space used: 209300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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