Align Alpha-ketoglutaric semialdehyde dehydrogenase 3; alphaKGSA dehydrogenase 3; 2,5-dioxovalerate dehydrogenase 3; KGSADH-III; EC 1.2.1.26 (characterized)
to candidate CCNA_02881 CCNA_02881 oxoglutarate semialdehyde dehydrogenase
Query= SwissProt::Q08IB7 (530 letters) >FitnessBrowser__Caulo:CCNA_02881 Length = 528 Score = 663 bits (1711), Expect = 0.0 Identities = 344/521 (66%), Positives = 399/521 (76%), Gaps = 2/521 (0%) Query: 3 LTGHLLIGQSAIAGQNGTLHAIAAATGEPLDPAFGGASLHDLDTACALADDAFDTYRDTS 62 LTG LLIG G +G + + ATGE L+PAFGGA+ D++ ACALA +AF YR Sbjct: 4 LTGELLIGGERRFGIHGEIKGVNPATGETLEPAFGGATTADVEAACALAAEAFGPYRSLP 63 Query: 63 LEARAAFLDAIGRHIMALGDELIERCVIETGLPRARIEGERGRTVGQLALFASLVRDGGF 122 E RA FL++I HI A+GD+LI R + ETGLPR R+EGERGRTVGQL LFA ++RDGGF Sbjct: 64 YETRAQFLESIAEHIEAIGDDLIVRTMAETGLPRPRLEGERGRTVGQLRLFAGVLRDGGF 123 Query: 123 LDARIDPARPERKPLPRVDLRLRNIAVGPVAVFGASNFPLAFSVAGGDTASALAAGCPVI 182 L+ARIDPA P+RKPLPR DLRLRN+ +GPVAVFGASNFPLAFSVAGGDTASALAAGCPVI Sbjct: 124 LEARIDPAMPDRKPLPRPDLRLRNVPLGPVAVFGASNFPLAFSVAGGDTASALAAGCPVI 183 Query: 183 VKAHSAHPGTSALVGRAIQQAARECGMPAGVFSLLFDASREIGQALVADPRIKAVGFTGS 242 VKAH AHPG S LVGRAIQ A CG+P GVF+L+ D+ E+ QALVADPR+KA GFTGS Sbjct: 184 VKAHPAHPGASELVGRAIQAAVAACGLPPGVFALIHDSGYEVSQALVADPRVKAAGFTGS 243 Query: 243 RRGGVALMHIAAARPEPIPVYAEMSSINPVLLLPAALDARHDAIAPQFVASLTLGAGQFC 302 RRGG+AL+ IA RPEPIP YAEMSSINPV+LLPAAL AR D IAP FVA+LTLGAGQFC Sbjct: 244 RRGGLALLAIAQGRPEPIPFYAEMSSINPVILLPAALKARADKIAPDFVAALTLGAGQFC 303 Query: 303 TNPGLVLAVDGPALRAFEEAAAAAVRAAPAQTMLTPHIHASYEQGVAALRDHAAVELLAQ 362 TNPGL+LA+DGP L AF EAA AV AAPA MLTP I ++ GVAAL D A V +A+ Sbjct: 304 TNPGLILAIDGPELDAFIEAAGKAVEAAPASVMLTPGICQAFAHGVAALTDAAEVTTVAR 363 Query: 363 GAEG--NRLQARAALLATSAEAFITHPELRDEVFGPASLIVRCPDADTLHRVLKSLEGQL 420 G G RAAL + +A F+ +P L +EVFG ASL+VRC L V+ +LEGQL Sbjct: 364 GVPGPDGSHTGRAALFSVTAADFLANPHLHEEVFGAASLVVRCAGQAELEAVIAALEGQL 423 Query: 421 TIAAHLADGDAPLFAALRPLLERKAGRILVNGFGTGVEVGHAMVHGGPFPATSDTRTTSV 480 TIA H+ + D + AL P LE KAGRILVNGFGTGVEV AMVHGGPFP+TSD RTTSV Sbjct: 424 TIALHMDEADHGIAGALLPALELKAGRILVNGFGTGVEVAPAMVHGGPFPSTSDGRTTSV 483 Query: 481 GARAIERFLRPVSYQDLPDALLPEAIRSGNPLNVPQRIDGV 521 G AI RFLRPVSYQ+LP+ALLP +++ NPL V +R+DGV Sbjct: 484 GTLAIARFLRPVSYQNLPEALLPAELKTQNPLGVVRRVDGV 524 Lambda K H 0.321 0.136 0.398 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: 961 Number of extensions: 45 Number of successful extensions: 2 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: 530 Length of database: 528 Length adjustment: 35 Effective length of query: 495 Effective length of database: 493 Effective search space: 244035 Effective search space used: 244035 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 (21.9 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