Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_086511804.1 BZY95_RS20815 NAD-dependent succinate-semialdehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >NCBI__GCF_002151265.1:WP_086511804.1 Length = 495 Score = 206 bits (523), Expect = 2e-57 Identities = 156/478 (32%), Positives = 223/478 (46%), Gaps = 35/478 (7%) Query: 4 KQQLLIDGAWVDG-DAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPDWARRSF 62 +Q IDG+WVD D A DP S L + + QV A+ +A +A P W R+ Sbjct: 22 RQHAYIDGSWVDASDEAIIEVVDPASDTRLGSVPRLTQAQVREAIESADRALPQWKARTA 81 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEARTEVGAMIGKVAISITAYHERTGE 122 ER A++ R+ E H+E LA + E GKPL EAR E+ +A+ E E Sbjct: 82 KERAAILRRWYELCMAHQEDLARILTLEQGKPLAEARGEI--------TYGSAFIEWFAE 133 Query: 123 RARDI---------GDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKP 173 A+ I GD R V+ P GV+A P+NFP + A+ AG VV KP Sbjct: 134 EAKRIYGDVIPAHAGDRRIVVTKEPVGVVAAITPWNFPNAMITRKAAAAMAAGCTVVVKP 193 Query: 174 SEQTPMTADLTLQCWLEAGLPAGVINLVQGAAE-VGQALAGSADIDGLLFTGSAKVGGLL 232 + TP +A + AG+P GV+N+V G+A VG L + + L FTGS +VG +L Sbjct: 194 ASSTPFSALALAELAERAGVPRGVLNVVTGSARTVGDELTANPLVRKLSFTGSTEVGKVL 253 Query: 233 HRQFGGQVDKILALELGGNNPLVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHG 292 V K+ ++ELGGN P ++ D D + AV ++ S F + GQ C CA R+ V H Sbjct: 254 LAACAQTVKKV-SMELGGNAPFIIFDDADLDQAVAGVMASKFRNTGQTCVCANRIFV-HE 311 Query: 293 AVGDDLIDALTSAIAELRVAAPFSEPAPFYAGLTSVEAADGLLAAQ-----DDLVARGGR 347 + D + L A+A RV E G+T D A+ D RG Sbjct: 312 RIYADFAERLAQAVAAQRVGNGLEE------GVTLGPLIDPAAVAKVEEHIADARERGAS 365 Query: 348 PLSRMRRLQAGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYG 405 +R G + P ++ D + +EE FGP+ + R+ D E + LANDT YG Sbjct: 366 VYLGGQRHALGGNFFEPTILTDVSSDARLMNEETFGPVAPLLRFSDEQEVVRLANDTPYG 425 Query: 406 LSAGLIGGERADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYAAD 463 L++ + + GIV N +S APFGG+ +SG R + Y + Sbjct: 426 LASYFYTRDVGRVWRVAEALECGIVGINEGII-SSELAPFGGVKESGIGREGSKYGIE 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: 662 Number of extensions: 36 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: 495 Length adjustment: 34 Effective length of query: 455 Effective length of database: 461 Effective search space: 209755 Effective search space used: 209755 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 24 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