Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 207 bits (526), Expect = 1e-57 Identities = 151/451 (33%), Positives = 230/451 (50%), Gaps = 17/451 (3%) Query: 15 FIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLV 74 FIAG++ K ++PA+G+++ A VDAA+ +A+AA W A+ R Sbjct: 36 FIAGRFTQPKA-DLDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALPGWQALGGHGRAR 94 Query: 75 IVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTGTVENPM 134 + A A ++ HA L A L+ GK L ESR + + A+ E+ Sbjct: 95 HLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQ---ESEF 151 Query: 135 PGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQL 194 P H P GVV P+NFP + I PAL GNTV+ KP+E T A L +L Sbjct: 152 PD------HVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTALLFAEL 205 Query: 195 WQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254 QQAGLP GVLN++ G+ ATG A+ +H GI + FTGS+ G L+ +Q AG GK L LE Sbjct: 206 AQQAGLPAGVLNIVTGDGATGAAVVAHPGIQKIAFTGSTEVGRLIREQTAGS-GKSLTLE 264 Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314 +GG +P I+ E A++DAA+ ++ + + + GQ C RL + + + D +A+L T Sbjct: 265 LGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIH-DLFIARLKTRMQ 323 Query: 315 KIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG-FVTPGI 373 K+ +G P + GA+IS V++ + G ++ TP G F P + Sbjct: 324 KLKVGAPLDKCSD-MGALIS-PVQLERVRSLVEQGVREGAQCHQVVLDTPPGGCFYPPTL 381 Query: 374 I-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQHFYRR 432 + V A+ +A EE FGP+L + D A+ ANN+ +GL+A + +++ + Sbjct: 382 LTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETIGLALGVAPQ 441 Query: 433 IRAGIVNWNKPITGASSAAPFGGIGASGNHR 463 ++AG+V W +A FGG+ SG R Sbjct: 442 LKAGVV-WINSTNQFDAAVGFGGVRESGYGR 471 Score = 64.7 bits (156), Expect = 1e-14 Identities = 65/224 (29%), Positives = 96/224 (42%), Gaps = 6/224 (2%) Query: 11 TQTQFIAGQWLAGKGPSFSSVNPANGEVIWQ-GLGADAGQVDAAITSARAAFYTWSAMSL 69 T +I G+ + G + + GE + GLG +A + +A W++ S Sbjct: 517 TAKLYIGGKQVRPDGEVSMACHSTQGERLEDVGLGNRKDIRNAVAAAVKAG--GWTSASP 574 Query: 70 TERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAER-TG 128 R + AE L E FAR IA TG E+R EV A ++ + A A++ G Sbjct: 575 HRRAQGLYYIAENLSARTEEFARRIASTTGVTADEARAEVDASIKRL-FTYGAWADKFEG 633 Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188 V P A + GVV V P P + P + GN V+ PSE P VA Sbjct: 634 AVHQPPMRGVALAMPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVA 693 Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTG 231 Q+ + LP GV+N++ G+ A LA H ++ L+ G Sbjct: 694 TDLYQVLDTSDLPAGVINIVTGKSAELLPVLAEHDEVEALWVRG 737 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: 975 Number of extensions: 47 Number of successful extensions: 6 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: 793 Length adjustment: 38 Effective length of query: 460 Effective length of database: 755 Effective search space: 347300 Effective search space used: 347300 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