Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 211 bits (536), Expect = 6e-59 Identities = 158/458 (34%), Positives = 229/458 (50%), Gaps = 13/458 (2%) Query: 12 QTQFIAGQWL-AGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLT 70 Q +I G ++ A +F S+NPANGEV+ Q A A ++ A+ SA W+A++ Sbjct: 7 QQLYIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQGQRIWAALTGI 66 Query: 71 ERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKAN-AERTGT 129 ER I+ + L+E + A L+TGK L E+R+ V +TG + A A Sbjct: 67 ERARIMRRAVDLLRERNDELALLETLDTGKPLSETRS-VDIVTGADVLEYYAGLAPAIEG 125 Query: 130 VENPMPGAK-AFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188 + P+ + + R +P GVVA G +N+P + PAL AGN ++FKPSE+T A Sbjct: 126 EQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSA 185 Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247 +++ +AGLP+GV N+L G A G + H I + FTG TG + A Sbjct: 186 LKLAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSS 245 Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307 K + +E+GG +PLII E A++D A + + F SSGQ CT R+F+P A A Sbjct: 246 LKDVTMELGGKSPLIICEDADLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKA-AFEA 304 Query: 308 KLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGL- 366 KLL +I LGDP E + FG ++S ++ A +AAG L +VT G Sbjct: 305 KLLERVQRIRLGDPQQE-ETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEY 363 Query: 367 ---GFVTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADS 422 FV P I D +D + EE FGP+L + Y D D I AN+T +GL+AG++ Sbjct: 364 AKGAFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTAD 423 Query: 423 ETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460 R+ AGI W + + P GG SG Sbjct: 424 LARAHRIIHRLEAGIC-WINTWGESPAQMPVGGYKQSG 460 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: 566 Number of extensions: 23 Number of successful extensions: 5 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: 498 Length of database: 490 Length adjustment: 34 Effective length of query: 464 Effective length of database: 456 Effective search space: 211584 Effective search space used: 211584 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: 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