Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate BWI76_RS07615 BWI76_RS07615 betaine-aldehyde dehydrogenase
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__Koxy:BWI76_RS07615 Length = 490 Score = 201 bits (512), Expect = 4e-56 Identities = 152/459 (33%), Positives = 226/459 (49%), Gaps = 15/459 (3%) Query: 12 QTQFIAGQWL-AGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLT 70 Q +I G ++ A G +F ++NPANGEV+ A VD A+ SA+ W+AMS Sbjct: 7 QQLYIDGGYVSATSGKTFETINPANGEVLATVQAAGREDVDRAVKSAQKGQKIWAAMSAM 66 Query: 71 ERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANA--ERTG 128 ER I+ + L+ + AR L+TGK L E+ V +TG + A G Sbjct: 67 ERSRILRKAVDILRARNDELARLETLDTGKPLSETAA-VDIVTGADVLEYYAGLIPALEG 125 Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188 + + + R +P GVVA G +N+P + PAL AGN ++FKPSE+TP A Sbjct: 126 SQIPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTA 185 Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQP 247 +++++AGLP GV N+L G A TG+ L H I + FTG +G + A Sbjct: 186 LKLAEIYREAGLPAGVFNVLPGTGAETGQYLTEHPDIAKISFTGGVASGKKVMANAAASS 245 Query: 248 GKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILA 307 K + +E+GG +PLI+ E A++D A + + F SSGQ CT R+F+P T A Sbjct: 246 LKEVTMELGGKSPLIVCEDASLDLAADIAMMANFYSSGQVCTNGTRVFVP-TRLKAAFEE 304 Query: 308 KLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG 367 K+L A+I GD FAE+ FG ++S +++ + G L+ + G G Sbjct: 305 KILARVARIRPGDLFAESTN-FGPLVSFPHRDNVLR-YIETGKQEGARLLCGGEALKGEG 362 Query: 368 F-----VTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLAD 421 F V P + D D + EE FGP++ + Y D + A+ AN T +GL+AG++ Sbjct: 363 FDRGAWVAPTVFTDCDDQMTIVREEIFGPVMSILSYDDEEEALRRANATEYGLAAGVVTP 422 Query: 422 SETDYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460 R+ AGI W + + P GG SG Sbjct: 423 DLNRAHRLIHRLEAGIC-WINTWGESPAEMPVGGYKHSG 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: 612 Number of extensions: 32 Number of successful extensions: 5 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: 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