Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 219 bits (559), Expect = 1e-61 Identities = 165/485 (34%), Positives = 240/485 (49%), Gaps = 49/485 (10%) Query: 4 KQQLLIDGAWVDGD-AARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 K + IDG WVD D A A +P +G + T A A Q + A+AAA +AF W R+ Sbjct: 13 KARCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAFGPWKDRTA 72 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122 +R ++ R+ E + H+E LA + E GKPL EAR E+ +Y E E Sbjct: 73 EDRARILRRWFELMLQHQEDLALIMTSEQGKPLAEARGEIAYA--------ASYIEWFAE 124 Query: 123 RARDIG---------DARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKP 173 AR I D R V+ P GV A P+NFP + + PAL AG ++ KP Sbjct: 125 EARRIYGEVIPSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKP 184 Query: 174 SEQTPMTADLTLQCWLEAGLPAGVINLVQG-AAEVGQALAGSADIDGLLFTGSAKVGGLL 232 + QTP++A + AG+PAGV +++ G A +G L S + L FTGS ++G +L Sbjct: 185 ATQTPLSALAMAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVL 244 Query: 233 HRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHG 292 Q + K ++LELGGN P +V + D +AAV + S + + GQ C CA RL+V G Sbjct: 245 AAQCAPTLKK-MSLELGGNAPFIVFEDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDG 303 Query: 293 AVGDDLIDALTSAIAELRVAAPFSE-----PAPFYAGLTSVEAADGLLAAQDDLVARGGR 347 V D + L +A L+V E P A LT VEA L+A D ARG R Sbjct: 304 -VYDAFAEKLARTVAALKVGHGLEEGVEQGPLIDEASLTKVEA---LVA---DAKARGAR 356 Query: 348 PLSRMRRLQAGTSLLSPGLI-DVT-GCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYG 405 ++ RR G + P ++ D+T + EE FGP+ + R+ EAI +ANDT +G Sbjct: 357 VVTGGRRHALGGTFYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFG 416 Query: 406 LSA-------GLIGGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSA 458 L+A G + ++ I AG++ +++ APFGG+ SG R + Sbjct: 417 LAAYFYSRDVGRVWRVSGALQYGMVGINAGVI--------STAVAPFGGVKQSGMGREGS 468 Query: 459 YYAAD 463 + + Sbjct: 469 VHGIE 473 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: 616 Number of extensions: 26 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: 486 Length adjustment: 34 Effective length of query: 455 Effective length of database: 452 Effective search space: 205660 Effective search space used: 205660 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