Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 190 bits (483), Expect = 8e-53 Identities = 151/465 (32%), Positives = 226/465 (48%), Gaps = 22/465 (4%) Query: 11 GAWVDGDA-ARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSFAERQAVV 69 GAW D D+ A F T+P G+ + + A+AAA A WA R+ +R V+ Sbjct: 26 GAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVL 85 Query: 70 ERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERT--GER-ARD 126 R+ + + + + LA + E GKPL EAR EV M G + A + GE Sbjct: 86 RRWFDLIVGNADDLARILTAEMGKPLAEARGEV--MYGASFVEWFAEEAKRLYGETIPGH 143 Query: 127 IGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTADLTLQ 186 + DAR + +P GV+ P+NFP + PAL AG A + KP+E TP++A Sbjct: 144 LPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAV 203 Query: 187 CWLEAGLPAGVINLV--QGAAEVGQALAGSADIDGLLFTGSAKVGGLLHRQFGGQVDKIL 244 AG+PAG+ ++ ++ +G+ + + L FTGS +VG +L Q QV K Sbjct: 204 LAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKK-C 262 Query: 245 ALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLIDALTS 304 ++ELGGN P +V D D + AV + F + GQ C CA R+ V G V D + L + Sbjct: 263 SMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDG-VYDAFAEKLAA 321 Query: 305 AIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQDDLVARGGRPLSRMRRLQAGTSLLSP 364 A+ EL+V +E L ++ A + + DDL A+GG ++ G + +P Sbjct: 322 AVEELKVGDGAAEGVTI-GPLINMPAVEKVQDHLDDLRAKGGTVVTGGETHPLGGTFFTP 380 Query: 365 GLIDVTG----CDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGERADWDD 420 + VTG V EE FGP+ + R+ + DE IA+ANDT +GL+ + Sbjct: 381 TV--VTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITR 438 Query: 421 FLLRIRAGIVNWNRQTTG--ASSDAPFGGIGDSGNHRPSAYYAAD 463 + GIV N TG ++ APFGG+ SG R + + D Sbjct: 439 VSEALEYGIVGIN---TGIISTEGAPFGGVKQSGLGREGSRHGID 480 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: 646 Number of extensions: 25 Number of successful extensions: 6 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: 492 Length adjustment: 34 Effective length of query: 455 Effective length of database: 458 Effective search space: 208390 Effective search space used: 208390 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