Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate WP_012755647.1 RLEG_RS26480 aldehyde dehydrogenase (NADP(+))
Query= SwissProt::Q08IC0 (525 letters) >NCBI__GCF_000023185.1:WP_012755647.1 Length = 505 Score = 495 bits (1274), Expect = e-144 Identities = 264/506 (52%), Positives = 339/506 (66%), Gaps = 7/506 (1%) Query: 4 TGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQP 63 +G I E +AG+ T R+ +P+ G+ D F V V+RAC A AF + A Sbjct: 6 SGRHFIAGEWIAGTT-TFRS-EPAHGQAHD---FAVGTTELVDRACRAAEAAFAVFSATT 60 Query: 64 LAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGRF 123 R FLEAIA+EI G+A+ ETGLP RL GER RT GQL+LFA +R G Sbjct: 61 REERGIFLEAIAEEIDKRGEAVTLIGTQETGLPEGRLNGERARTTGQLKLFADHIRKGAH 120 Query: 124 LAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPVI 183 L A +D AQP R P PR ++RL + +GPV VFGASNFPLAFS AGGDTA+ALAAGCPV+ Sbjct: 121 LDARVDAAQPDRQPAPRPEIRLVQRPIGPVAVFGASNFPLAFSTAGGDTAAALAAGCPVV 180 Query: 184 VKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTGS 243 VK H AH GT E++ AI AA+ +TGMPAGVFSL+ G R +G ALV+HPA++AVGFTGS Sbjct: 181 VKGHSAHPGTGEIIAEAIAAAIERTGMPAGVFSLIQGGRRDVGTALVTHPAIKAVGFTGS 240 Query: 244 RQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQFC 303 GG AL + RP+PIP + E+ S+NP+ L PAA AAR +AI +G+ SLTLG GQFC Sbjct: 241 LAGGRALFDLCAQRPEPIPFFGELGSVNPMFLLPAATAARAEAIGSGWAGSLTLGAGQFC 300 Query: 304 TNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIGA 363 T PG+ + +DGP+ D+F + A AL K MLT+GIA AY G ++ V + A Sbjct: 301 TKPGIAVVVDGPEADKFTSAAKAALEKVAPQTMLTKGIASAYHEGVERMRTSNAVAPVLA 360 Query: 364 GEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQLT 423 ++A +A L+E A+LA+ + S EVFGP L+VR +++ + E+ +GQLT Sbjct: 361 AQSAGR--EATPNLFETNGSAWLADHSLSEEVFGPLGLVVRVGSPEKLLTLAESFQGQLT 418 Query: 424 ATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTSVG 483 AT+ MD D LAR LLP+LERKAGR+LVNG+PTGVEV D+MVHGGP+PA++N TSVG Sbjct: 419 ATIHMDDADLGLARDLLPILERKAGRVLVNGFPTGVEVVDSMVHGGPYPASTNFGATSVG 478 Query: 484 ATAIERFLRPVCYQDFPDDLLPEGLQ 509 +I RFLRPV YQ+FP DLLP+ L+ Sbjct: 479 TMSIRRFLRPVAYQNFPADLLPQDLR 504 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: 898 Number of extensions: 53 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: 505 Length adjustment: 35 Effective length of query: 490 Effective length of database: 470 Effective search space: 230300 Effective search space used: 230300 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 24 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