Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate 7023382 Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__ANA3:7023382 Length = 487 Score = 177 bits (450), Expect = 6e-49 Identities = 152/489 (31%), Positives = 228/489 (46%), Gaps = 25/489 (5%) Query: 30 GGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLGEELR 89 G D+ S +P E I +T +A + ++ A EA W ++ R ++V +L Sbjct: 14 GHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDGRLKIVEAYRSQLE 73 Query: 90 AFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATER---PGHRMM 146 A KA+L ++ E GK E EV MI +GLS Y TE P R + Sbjct: 74 ANKAELAETIAQETGKPQWETATEVAAMIG----KIGLSATAYNKRTGTEANDTPAGRAV 129 Query: 147 ETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIA 206 P GVV + +NFP + + + AL+ G+ VV+KPSE TP A ++ E+A Sbjct: 130 LRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELMVSLWEKA-- 187 Query: 207 RFGDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAI-LEL 265 P G+ ++ G+ G+ L HP++ + TGS+R G + + A + + LE+ Sbjct: 188 ---GLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKILALEM 244 Query: 266 GGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVY-DQLVPRLKKAYQS 324 GGNN I+ AD+ A+ I A ++GQRCT RRL+V + D LV +L +A + Sbjct: 245 GGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVEAVKQ 304 Query: 325 VSVGN-PLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELGH--ENGYYVKP 381 + VG + +G ++ +AA GM A A +N GG VEL H V P Sbjct: 305 IKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGV----SLVELSHLQAGTGLVSP 360 Query: 382 ALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLA 441 L+++ EE F P+L +++YSDFD + N GLS+ I + E FLA Sbjct: 361 GLIDVTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSRDDYEYFLA 420 Query: 442 ADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDA--WKAYMRRATNTVNYSKAL 499 GI N N +GA FGG +G R S A + AY + S Sbjct: 421 R--IRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPA 478 Query: 500 PLAQGVSFD 508 L+ G+S + Sbjct: 479 SLSPGLSLE 487 Lambda K H 0.317 0.134 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: 546 Number of extensions: 33 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: 510 Length of database: 487 Length adjustment: 34 Effective length of query: 476 Effective length of database: 453 Effective search space: 215628 Effective search space used: 215628 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