Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate PP_0213 PP_0213 succinate-semialdehyde dehydrogenase (NADP+)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Putida:PP_0213 Length = 480 Score = 211 bits (538), Expect = 3e-59 Identities = 157/478 (32%), Positives = 241/478 (50%), Gaps = 37/478 (7%) Query: 4 KQQLLIDGAWVDGDAARFAK-TDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 +QQ I+G W+D D + K T+P +GE + T + A+ AA +A P W + Sbjct: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122 ER A + R+ E + +++ LA + E GKPL EA+ G++A + + E Sbjct: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAK-------GEIAYAASFIEWFAEE 122 Query: 123 RARDIGDA--------RAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPS 174 R GD R ++ +P GV A P+NFP + PAL AG +V KP+ Sbjct: 123 AKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182 Query: 175 EQTPMTADLTLQCWLEAGLPAGVINLVQGAA-EVGQALAGSADIDGLLFTGSAKVGGLLH 233 QTP +A ++ AG+PAGV+++V G+A EVG L G++ + L FTGS ++G L Sbjct: 183 SQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLM 242 Query: 234 RQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGA 293 + + K+ +LELGGN P +V D D + AV + S + + GQ C CA R+ V G Sbjct: 243 EECAKDIKKV-SLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDG- 300 Query: 294 VGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQ-----DDLVARGGRP 348 V D + L +A+A+L++ E G T+ DG A+ +D V++G + Sbjct: 301 VYDAFAEKLAAAVAKLKIGNGLEE------GTTTGPLIDGKAVAKVQEHIEDAVSKGAKV 354 Query: 349 LSRMRRLQAGTSLLSPGLIDV-TGCDVPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLS 407 LS + ++ G L+DV V EE FGPL + R++D E IA++NDT +GL+ Sbjct: 355 LSGGKLIE-GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLA 413 Query: 408 AGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSD--APFGGIGDSGNHRPSAYYAAD 463 + + + + G+V N TG S+ APFGGI SG R + Y + Sbjct: 414 SYFYARDMSRVFRVAEALEYGMVGIN---TGLISNEVAPFGGIKASGLGREGSKYGIE 468 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: 613 Number of extensions: 43 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: 480 Length adjustment: 34 Effective length of query: 455 Effective length of database: 446 Effective search space: 202930 Effective search space used: 202930 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