Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 201 bits (512), Expect = 6e-56 Identities = 152/486 (31%), Positives = 237/486 (48%), Gaps = 25/486 (5%) Query: 15 FIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLV 74 FI G + A G +F++ NPA G + Q ++AA+T+AR A W+ + Sbjct: 36 FIGGTFQA-PGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWAR 94 Query: 75 IVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTGTVENPM 134 ++ A A L++H+ LFA L+ GK + ESR + + +A +E+ + Sbjct: 95 VLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQR---HFYYHAGMAALMEDEL 151 Query: 135 PGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQL 194 P P GV P+NFP + I PAL GNTV+ KP+E TP A L ++ Sbjct: 152 PD------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTALLFAEI 205 Query: 195 WQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254 +AG+P GV+N++ G+ ATG AL SH G+D + FTGS++ G + + AG GK L LE Sbjct: 206 CGEAGVPPGVVNIVTGDGATGAALVSHPGVDKIAFTGSTDVGREIRRATAG-TGKALTLE 264 Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314 +GG +P ++ E A++D+AV ++ + + + GQ C RL + + +A AKL A Sbjct: 265 LGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLV-QEGIAEAFYAKLRARMA 323 Query: 315 KIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG-FVTPGI 373 + +GDP + GAM+ A + + AG + P G F P + Sbjct: 324 TLRIGDPLDKCID-VGAMVDPAHCAKVAE-----MVAGSNGEVHQPGTVPAEGAFYPPTL 377 Query: 374 I-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQHFYRR 432 I + A PL +E FGP+L + A++ AN T +GL+A L +++ + Sbjct: 378 ITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDIAPK 437 Query: 433 IRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYA----ADYCAYPVSSVEAQAVSLP 488 + AG+V W +AA FGG+ SG R + A P + V A+ P Sbjct: 438 LAAGVV-WVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTKQAAPPKALVPVAAIPAP 496 Query: 489 ASLSPG 494 A+ PG Sbjct: 497 AAPKPG 502 Score = 61.6 bits (148), Expect = 1e-13 Identities = 52/185 (28%), Positives = 82/185 (44%), Gaps = 3/185 (1%) Query: 63 TWSAMSLTERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKA 122 +W + R I+ AE L E FA IA TG + + EV A ++ + A Sbjct: 558 SWGRTTGHLRAQILYYVAENLSARTEEFATRIAEMTGSRVPRAEAEVSAAIDRL-FTYAA 616 Query: 123 NAERTGTVENPMP-GAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPS 181 A++ P+P A +P GV+ F P + P + AL GN ++ PS Sbjct: 617 WADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGAVSILGAALAMGNRLVLVPS 676 Query: 182 ELTPKVAELTMQLWQQAGLPNGVLNLLQG-EIATGKALASHKGIDGLFFTGSSNTGHLLH 240 E P A Q+ + +P GV+N++ G A K LASH G+D ++ ++ + Sbjct: 677 EPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASHLGVDAVWSFSGADISTTIE 736 Query: 241 QQYAG 245 + AG Sbjct: 737 AEAAG 741 Lambda K H 0.317 0.133 0.390 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: 966 Number of extensions: 50 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: 2 Length of query: 498 Length of database: 780 Length adjustment: 37 Effective length of query: 461 Effective length of database: 743 Effective search space: 342523 Effective search space used: 342523 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 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