Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate RR42_RS04830 RR42_RS04830 2,5-dioxovalerate dehydrogenase
Query= SwissProt::Q08IC0 (525 letters) >FitnessBrowser__Cup4G11:RR42_RS04830 Length = 525 Score = 644 bits (1662), Expect = 0.0 Identities = 341/523 (65%), Positives = 397/523 (75%), Gaps = 2/523 (0%) Query: 1 MQLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYR 60 M +TGEMLIGA AV G+ L A +P+ GE + AP F A+ ERAC LA AFD YR Sbjct: 1 MTITGEMLIGASAVRGTTKILHATNPATGEVL-APEFHGGGAAEAERACALAEAAFDTYR 59 Query: 61 AQPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRD 120 RA FLE+IA + ALGD LIERAHAE+ LPVARLQGER RT GQLRLFA V+RD Sbjct: 60 NTSPETRARFLESIASGLEALGDTLIERAHAESALPVARLQGERARTAGQLRLFASVLRD 119 Query: 121 GRFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGC 180 GR+ +A++D A P RTP PR DLRLQK+ +GPV VFGASNFPLAFSVAGGDTASALAAGC Sbjct: 120 GRWQSATLDSALPERTP-PRPDLRLQKIAVGPVAVFGASNFPLAFSVAGGDTASALAAGC 178 Query: 181 PVIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGF 240 PV+VKAH AHLGTSELVGR I+ AVA G+P GVFSLLVG G +G ALV+HP++QAVGF Sbjct: 179 PVVVKAHSAHLGTSELVGRVIQKAVADAGLPEGVFSLLVGAGVAVGTALVAHPSIQAVGF 238 Query: 241 TGSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVG 300 TGSR GG+ALVQ AN+RPQPIPVYAEMSSINPV L PAALAARG IA VDSL +GVG Sbjct: 239 TGSRSGGLALVQTANSRPQPIPVYAEMSSINPVFLLPAALAARGAQIARNLVDSLVMGVG 298 Query: 301 QFCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVRE 360 QFCTNPGL+LA++ P LD F A ALA+K A MLT GI+ AY NG +L+++ G+R Sbjct: 299 QFCTNPGLLLAVESPALDVFRQGAIAALAEKAAATMLTPGISQAYDNGVAQLSDIEGLRR 358 Query: 361 IGAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420 IG+G+ A QA AL+E A+ FLA+ EVFGP+S++V CRD +E+ V LEG Sbjct: 359 IGSGQTASGPNQARPALFETTAERFLADHRMEAEVFGPSSVLVVCRDHEEMLAVARRLEG 418 Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480 QLTAT+Q DA D+ A LL VLERKAGR+L NGYPTGVEV AMVHGGPFPATS+ T Sbjct: 419 QLTATVQADAGDRAEAGSLLTVLERKAGRVLFNGYPTGVEVSYAMVHGGPFPATSDTRAT 478 Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523 SVGA+AIERFLRPVCYQ+ P +LLP LQ+ NPL + RL DG+ Sbjct: 479 SVGASAIERFLRPVCYQNVPAELLPPALQDGNPLKVWRLTDGQ 521 Lambda K H 0.320 0.137 0.396 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: 908 Number of extensions: 42 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: 525 Length adjustment: 35 Effective length of query: 490 Effective length of database: 490 Effective search space: 240100 Effective search space used: 240100 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