Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= curated2:Q1QTQ7 (489 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 211 bits (537), Expect = 5e-59 Identities = 164/467 (35%), Positives = 228/467 (48%), Gaps = 15/467 (3%) Query: 6 QLLIDGAWVDG-DAARFAKTDPVSGETLWTATAASATQVEHAVAAARQAFPD--WARRSF 62 Q +IDG V+ A F P G+ L TA A VE AVA AR AF D W + Sbjct: 22 QAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAFEDGRWRDQGP 81 Query: 63 AERQAVVERFRECLETHREHLATAIAQETGKPLWEART-EVGAMIGKVAISITAYHERTG 121 +++AV+ R E +E + LA + + GKP+ +AR ++ I A + G Sbjct: 82 RQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRWYAEALDKVYG 141 Query: 122 ERARDIGDARAVLRHRPHGVLAVYGPYNFPGHLPNGHIVPALLAGNAVVFKPSEQTPMTA 181 E D + H P GV+ P+NFP H+ + PAL GN+VV KP+EQ+P+TA Sbjct: 142 EVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVLKPAEQSPLTA 201 Query: 182 DLTLQCWLEAGLPAGVINLVQGAAEV-GQALAGSADIDGLLFTGSAKVGGLLHRQFGGQV 240 LEAGLP GV+N++ G V G+ALA S D+D + FTGS VG L Sbjct: 202 LKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGRRLMEYSARSN 261 Query: 241 DKILALELGGNNP-LVVKDVPDREAAVLSILQSAFASGGQRCTCARRLIVPHGAVGDDLI 299 K ++LELGG +P +V D PD EAA + F + G+ CT A RL+V + D + Sbjct: 262 LKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLV-EAPIKDAFL 320 Query: 300 DALTSAIAELRVAAPFSEPAPFYAGLT--SVEAADGLLAAQDDLVARGGRPLSRMR-RLQ 356 + ++V P F A ++ + A +A D AR R L R R + Sbjct: 321 ARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGAR--RVLGGQRVRQE 378 Query: 357 AGTSLLSPGLIDVTGCD--VPDEEHFGPLLKVHRYRDWDEAIALANDTRYGLSAGLIGGE 414 AG + P + D D + EE FGP+L V + DEA+ LANDT YGL+AGL + Sbjct: 379 AGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLAAGLWTAD 438 Query: 415 RADWDDFLLRIRAGIVNWNRQTTGASSDAPFGGIGDSGNHRPSAYYA 461 + R++AG+V W PFGG SG R + +A Sbjct: 439 VSKALRGARRLKAGLV-WVNGWDACDITMPFGGFKQSGFGRDRSLHA 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: 598 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 489 Length of database: 499 Length adjustment: 34 Effective length of query: 455 Effective length of database: 465 Effective search space: 211575 Effective search space used: 211575 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