Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate 6937359 Sama_1529 fatty aldehyde dehydrogenase (RefSeq)
Query= metacyc::G1G01-1343-MONOMER (525 letters) >FitnessBrowser__SB2B:6937359 Length = 515 Score = 417 bits (1072), Expect = e-121 Identities = 222/492 (45%), Positives = 308/492 (62%), Gaps = 3/492 (0%) Query: 17 SRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETSLEQRAEFLEAIATQ 76 S + +P+T L A+ GT V A A AAF +++TS +Q+A+ LE +A + Sbjct: 18 SEASFTRFNPSTNSVLPGAFSQGTVVEVEAAAIAADAAFWEFQQTSADQKAKLLETMAKE 77 Query: 77 IEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEWLDVRIDSALPERQP 136 IE GDA++ A++E+GLP+AR++GE GRT QLR FA +R + + +D A P+RQP Sbjct: 78 IEQDGDAIVACAMLESGLPEARLKGELGRTAGQLRLFASVLRE-PYSPLLMDKANPDRQP 136 Query: 137 LPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVVVKAHSAHPGTSELV 196 LP+ +L+ Q+ LG VAVFGASNFPLAFS AGGDTASALAAGC V+VK H +HPGTSELV Sbjct: 137 LPKPELKLGQLPLGVVAVFGASNFPLAFSTAGGDTASALAAGCAVIVKGHPSHPGTSELV 196 Query: 197 GQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGSRSGGMALCQAAQAR 256 +A+A+A+ G+P+G+FSL+ GS + +ALV P +KAVGFTGS G L R Sbjct: 197 ARAMARAIDLTGMPKGLFSLIQGSEPALSVALVEHPLVKAVGFTGSLKVGRLLADRCALR 256 Query: 257 PEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFCTNPGLVIARQGPAL 316 PEPIP Y E+ S+NP L L A LA+ V S+ G GQFCT+PGLVIA +GP L Sbjct: 257 PEPIPFYGELGSVNPQLLLPGKLARDAAVLAEAQVNSMMMGHGQFCTSPGLVIAIKGPGL 316 Query: 317 QRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAITSGQAGQGPNQCQAQL 376 + ++ A + + A ML+ GI A+ ++ L P I GQA + + + + Sbjct: 317 ESYLAALSDIASRQNAAAMLSAGICQAFNQDVSILV--PRVNVIAQGQAAEAAHHSRPLI 374 Query: 377 FVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQLTATLQLDEADIDSAR 436 +A A P L E+FG +LV C E++ ++ + L GQLT ++ E ++ Sbjct: 375 ASIEASALFGQPELLEEIFGPFALVAICDSKEEMFELVKRLPGQLTGSIHGLETEVADFG 434 Query: 437 ALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSVGTAAILRFLRPVCYQ 496 ++ L K GRI+ N PTGVEV AM HGGP+PA++D R+TSVG A+ RF+RP+CYQ Sbjct: 435 DIIDRLAFKVGRIMFNQMPTGVEVARAMNHGGPYPASTDGRSTSVGAEAMKRFMRPICYQ 494 Query: 497 DVPDALLPQALK 508 ++P+ LLP LK Sbjct: 495 NMPETLLPNELK 506 Lambda K H 0.319 0.134 0.391 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: 680 Number of extensions: 21 Number of successful extensions: 3 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: 525 Length of database: 515 Length adjustment: 35 Effective length of query: 490 Effective length of database: 480 Effective search space: 235200 Effective search space used: 235200 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 (21.8 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