Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 196 bits (498), Expect = 2e-54 Identities = 146/456 (32%), Positives = 221/456 (48%), Gaps = 22/456 (4%) Query: 18 GQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLVIVE 77 G A G +F ++NPANG V+ A VD A+ SA+ W++M+ ER I+ Sbjct: 14 GYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWASMTAMERSRILR 73 Query: 78 AFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANA--ERTGTVENPMP 135 + L+E + A+ L+TGKA E+ T V +TG + A G+ Sbjct: 74 RAVDILRERNDELAKLETLDTGKAYSETST-VDIVTGADVLEYYAGLIPALEGSQIPLRE 132 Query: 136 GAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQLW 195 + + R +P GVVA G +N+P + PAL AGN ++FKPSE+TP A +++ Sbjct: 133 TSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPLTALKLAEIY 192 Query: 196 QQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254 +AGLP+GV N+L G A TG+ L H GI + FTG +G + A K + +E Sbjct: 193 SEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANSAASSLKEVTME 252 Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314 +GG +PLI+ + A++D A + + F SSGQ CT R+F+P A K+L Sbjct: 253 LGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKA-AFEQKILARVE 311 Query: 315 KIALGDPFAETQPFFGAMIS----DKAAAGMVKAQADIQAAGGVSLIELTQVTPGLGF-- 368 +I GD F + Q FG ++S D + K + + G ++ V G GF Sbjct: 312 RIRAGDVF-DPQTNFGPLVSFPHRDNVLRYIAKGKEE-----GARVLCGGDVLKGDGFDN 365 Query: 369 ---VTPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSET 424 V P + D +D + EE FGP++ + Y D I AN+T +GL+AG++ Sbjct: 366 GAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIVTADLN 425 Query: 425 DYQHFYRRIRAGIVNWNKPITGASSAAPFGGIGASG 460 ++ AGI W + + P GG SG Sbjct: 426 RAHRVIHQLEAGIC-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: 601 Number of extensions: 34 Number of successful extensions: 4 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