Align Alpha-ketoglutaric semialdehyde dehydrogenase 3; alphaKGSA dehydrogenase 3; 2,5-dioxovalerate dehydrogenase 3; KGSADH-III; EC 1.2.1.26 (characterized)
to candidate RR42_RS23090 RR42_RS23090 2,5-dioxovalerate dehydrogenase
Query= SwissProt::Q08IB7 (530 letters) >FitnessBrowser__Cup4G11:RR42_RS23090 Length = 533 Score = 668 bits (1724), Expect = 0.0 Identities = 346/524 (66%), Positives = 400/524 (76%) Query: 1 MQLTGHLLIGQSAIAGQNGTLHAIAAATGEPLDPAFGGASLHDLDTACALADDAFDTYRD 60 M LTG LLIG+ ++ G +G + AI A+GE L PAFGGA+ LD ACALA AFD YR+ Sbjct: 1 MNLTGELLIGRQSVRGTHGEIRAIDPASGETLAPAFGGATRAQLDQACALAAQAFDGYRE 60 Query: 61 TSLEARAAFLDAIGRHIMALGDELIERCVIETGLPRARIEGERGRTVGQLALFASLVRDG 120 T L RAA L+ I +++ALGD LI RCV E+GLPRARIEGE GRT+ QL LFA +VR G Sbjct: 61 TPLAQRAALLEKIAANLLALGDALIARCVSESGLPRARIEGELGRTMSQLRLFAGVVRRG 120 Query: 121 GFLDARIDPARPERKPLPRVDLRLRNIAVGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180 FL RIDPA+P+R PLPRVDLRLR+IA+GPVAVFGASNFPLAFSVAGGDTASALAAGCP Sbjct: 121 DFLGLRIDPAQPQRMPLPRVDLRLRHIALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180 Query: 181 VIVKAHSAHPGTSALVGRAIQQAARECGMPAGVFSLLFDASREIGQALVADPRIKAVGFT 240 V+VKAH AHPGTS LVGRAIQ+A E G+P G FSLLFD+ EI Q LV+D RIKAVGFT Sbjct: 181 VVVKAHPAHPGTSELVGRAIQKAVEELGLPEGTFSLLFDSGLEIAQGLVSDHRIKAVGFT 240 Query: 241 GSRRGGVALMHIAAARPEPIPVYAEMSSINPVLLLPAALDARHDAIAPQFVASLTLGAGQ 300 GSR GG ALM +AAAR EPIPVYAEMSSINPVLL P AL R DAI F ASLTLGAGQ Sbjct: 241 GSRAGGTALMQLAAARSEPIPVYAEMSSINPVLLFPHALGNRADAIGKAFAASLTLGAGQ 300 Query: 301 FCTNPGLVLAVDGPALRAFEEAAAAAVRAAPAQTMLTPHIHASYEQGVAALRDHAAVELL 360 FCTNPGL+LAVDGP L F AA AA+ PA TMLTP IH +Y GV L H V + Sbjct: 301 FCTNPGLILAVDGPDLERFLAAAEAAIAQIPASTMLTPGIHRAYGAGVETLGCHPQVSTV 360 Query: 361 AQGAEGNRLQARAALLATSAEAFITHPELRDEVFGPASLIVRCPDADTLHRVLKSLEGQL 420 A+G G + Q +AAL +T+A+AF+ H LR EVFG ASL+VRCPD T+ RV++SLEGQL Sbjct: 361 ARGQAGAQYQGQAALFSTTAQAFLEHEALRAEVFGAASLVVRCPDLATMQRVVESLEGQL 420 Query: 421 TIAAHLADGDAPLFAALRPLLERKAGRILVNGFGTGVEVGHAMVHGGPFPATSDTRTTSV 480 T A H+ + D + P LER+ GRILVNGF TGVEV HAMVHGGP+P+TSD R+TSV Sbjct: 421 TAAIHIDEADYDTARSFLPALERRVGRILVNGFATGVEVSHAMVHGGPYPSTSDGRSTSV 480 Query: 481 GARAIERFLRPVSYQDLPDALLPEAIRSGNPLNVPQRIDGVPAP 524 G+ AI RFLRPV YQD+P ALLP+A+R+GNPL + R+DG P Sbjct: 481 GSLAIARFLRPVCYQDMPAALLPQALRAGNPLGLAVRVDGEMQP 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: 906 Number of extensions: 40 Number of successful extensions: 1 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: 533 Length adjustment: 35 Effective length of query: 495 Effective length of database: 498 Effective search space: 246510 Effective search space used: 246510 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