Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 192 bits (488), Expect = 2e-53 Identities = 157/478 (32%), Positives = 234/478 (48%), Gaps = 29/478 (6%) Query: 5 QQLLIDG-AWVDG---DAA---RFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPD- 56 Q+L I+G A+++G DA F PV G L + + AVA AR F Sbjct: 15 QRLEINGRAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESG 74 Query: 57 -WARRSFAERQAVVERFRECLETHREHLATAIAQETGKPLWEART-EVGAMIGKVAISIT 114 W+ +S +R+ V+ RF E LE H + LA + GKP+ ++ +V + S Sbjct: 75 VWSLQSPVKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGE 134 Query: 115 AYHERTGERARDIGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPS 174 A + E A + ++ P GV+A P+NFP + + PAL GN+VV KPS Sbjct: 135 AIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPS 194 Query: 175 EQTPMTADLTLQCWLEAGLPAGVINLVQGAAE-VGQALAGSADIDGLLFTGSAKVGGLLH 233 E++P+TA Q EAGLP GV+N++ G VGQALA D+D L+FTGS K+ L Sbjct: 195 EKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLM 254 Query: 234 RQFGGQVDKILALELGGNNP-LVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHG 292 G K + LE GG +P +V D PD +AA + + + G+ CT RL+V G Sbjct: 255 VYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESG 314 Query: 293 AVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLL----AAQDD---LVARG 345 V D+LI + + + P +PA + + D +L A D+ L+ G Sbjct: 315 -VKDELIKLIVKEMEAWQPGHPL-DPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGG 372 Query: 346 GRPLSRMRRLQAGTSLLSPGLID--VTGCDVPDEEHFGPLLKVHRYRDWDEAIALANDTR 403 + L+ + G ++P + D + EE FGP++ V + DEA+A+ANDT Sbjct: 373 SQVLA-----ETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTI 427 Query: 404 YGLSAGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYA 461 YGL+AG+ + + +R+G+V W G APFGG SGN R + +A Sbjct: 428 YGLAAGVWTSDISKAHKTAKALRSGMV-WINHYDGGDMTAPFGGYKQSGNGRDKSLHA 484 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: 640 Number of extensions: 29 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: 498 Length adjustment: 34 Effective length of query: 455 Effective length of database: 464 Effective search space: 211120 Effective search space used: 211120 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 Apr 09 2024. 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