Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 216 bits (549), Expect = 2e-60 Identities = 155/475 (32%), Positives = 225/475 (47%), Gaps = 25/475 (5%) Query: 41 YIGGEWVD--TKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDR 98 YI GEW D + E + NP A +E + + G+ E A+ AA A W+ ++R Sbjct: 14 YINGEWRDALSGETVTIANP-ATNEAIASVPVMGRDETREAIAAAEAALPAWRALTAKER 72 Query: 99 SRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVE 158 L + LM +L + E GK EA +V A FIE++A A R + Sbjct: 73 GAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYG---D 129 Query: 159 VVPYPGEDNESFYVPLGAGVV--IAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216 +P D + G GV I PWNFP A+ T +A G T+I KPA Sbjct: 130 TIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTA 189 Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 + E+ EAG PPGV + + G +G L E+P R ++FTGS VG+K+ + + A Sbjct: 190 LALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQ---QCA 246 Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336 P K+ +E GG IV AD D A EG ++S Y GQ C A+RL + G Y+ Sbjct: 247 P---TLKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYD 303 Query: 337 PVLERVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEG 394 +++ +L VG AE GP+++A KV S+++ ++G LV GGK L G Sbjct: 304 AFAQKLAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPLGG 363 Query: 395 EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKR 454 F+ P + T V ++A+EE FGP+ + R D + + ANDT +GL Y R Sbjct: 364 N--FMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDI 421 Query: 455 EHLEWARREFHVGNLYFNRKITGAL-VGVQPFGGFKLSG---TNAKTGALDYLRL 505 + G + N TG + V PFGG K SG +K G +Y+ + Sbjct: 422 SLIWKVAEALEYGMVGVN---TGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEI 473 Lambda K H 0.319 0.137 0.403 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: 575 Number of extensions: 28 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: 516 Length of database: 480 Length adjustment: 34 Effective length of query: 482 Effective length of database: 446 Effective search space: 214972 Effective search space used: 214972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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