Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate H281DRAFT_05316 H281DRAFT_05316 NADP-dependent aldehyde dehydrogenase
Query= SwissProt::Q08IC0 (525 letters) >FitnessBrowser__Burk376:H281DRAFT_05316 Length = 535 Score = 655 bits (1690), Expect = 0.0 Identities = 333/522 (63%), Positives = 393/522 (75%) Query: 2 QLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRA 61 ++TGEMLIG ++V G+ L AF+P+ G I PVFG DV ACELA+ AFD YR Sbjct: 10 RITGEMLIGRQSVRGAEEALHAFNPATGADIAEPVFGSGTARDVGLACELAQKAFDPYRQ 69 Query: 62 QPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDG 121 PL+ RA FLE IAD I ALGDAL+ERA E+GLP ARL+GERGRT GQL+LFA+ VR G Sbjct: 70 LPLSVRAEFLERIADGITALGDALVERAQQESGLPKARLEGERGRTTGQLKLFAQFVRSG 129 Query: 122 RFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCP 181 ++L A++D P R PLPRSDLR+QK+ +GPV VFGASNFPLAFSVAGGDTA+ALAAGCP Sbjct: 130 QWLDATLDSPLPERKPLPRSDLRMQKIAIGPVAVFGASNFPLAFSVAGGDTAAALAAGCP 189 Query: 182 VIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFT 241 V+VKAH AHLGTSE+VGR I+ + +P GVFSL+VG G +G ALV+HPA++AVGFT Sbjct: 190 VVVKAHRAHLGTSEMVGRVIQRVAQEMDLPEGVFSLIVGAGNSVGEALVAHPAIKAVGFT 249 Query: 242 GSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQ 301 GSR GG+AL+++A ARP+PIPV+AEMSSINPV L P AL R + IA GFVDSL LG GQ Sbjct: 250 GSRAGGLALMRVAAARPEPIPVFAEMSSINPVFLLPNALTQRTENIARGFVDSLVLGAGQ 309 Query: 302 FCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREI 361 FCTNPGL +A+D L F VA++AL KPA MLT GI AY G KLA +PGV + Sbjct: 310 FCTNPGLAIAVDSDALKNFVAVASEALGGKPAQTMLTSGIHSAYTQGESKLAGIPGVETV 369 Query: 362 GAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQ 421 G QA AL+ A+ FLA PA EVFGPAS IVRC+D +E+ +V E GQ Sbjct: 370 ARGVDVTGPNQARAALFVTDAKTFLATPALEDEVFGPASTIVRCKDENELLQVAEHFAGQ 429 Query: 422 LTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTS 481 LTAT+QMD+ D P ARRL+P+LERKAGRLLVNGYPTGVEVC AMVHGGPFPATS+ TS Sbjct: 430 LTATIQMDSADVPAARRLVPILERKAGRLLVNGYPTGVEVCHAMVHGGPFPATSDSRATS 489 Query: 482 VGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523 VG TAIERFLRPVCYQDFP DLLP+ L + NPL + R RDG+ Sbjct: 490 VGTTAIERFLRPVCYQDFPADLLPQALADDNPLDLWRRRDGE 531 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: 935 Number of extensions: 29 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: 525 Length of database: 535 Length adjustment: 35 Effective length of query: 490 Effective length of database: 500 Effective search space: 245000 Effective search space used: 245000 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