Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate 3609053 Dshi_2442 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::Q08IC0 (525 letters) >FitnessBrowser__Dino:3609053 Length = 501 Score = 495 bits (1274), Expect = e-144 Identities = 275/501 (54%), Positives = 332/501 (66%), Gaps = 9/501 (1%) Query: 5 GEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQPL 64 G+ LI A A GS T A DP+ G A F V A V++AC A DAF +Y Sbjct: 7 GKHLI-AGAWVGSDQTF-ASDPAHGP---AHEFSVGTPALVDQACAAAEDAFASYGYSDA 61 Query: 65 AARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGRFL 124 A RAAFL AIADEI A + ETGLP ARLQGERGRT GQLRLFA + G L Sbjct: 62 ATRAAFLNAIADEIDARAQIITGIGTQETGLPEARLQGERGRTTGQLRLFAEHILKGDCL 121 Query: 125 AASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPVIV 184 DPA P R PLPR DL+L + +GPV VFGASNFPLAFSVAGGDTA+ALAAGCPV+V Sbjct: 122 DRRHDPALPDRAPLPRPDLKLVQRPIGPVAVFGASNFPLAFSVAGGDTAAALAAGCPVVV 181 Query: 185 KAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTGSR 244 K H AH GT E+V AI AA+A+TGMPAGVFSL+ G R +G ALV HP ++AVGFTGS Sbjct: 182 KGHSAHPGTGEIVAEAIHAAIARTGMPAGVFSLIQGGKRDVGTALVQHPLIRAVGFTGSL 241 Query: 245 QGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQFCT 304 GG AL + ARP+PIP + E+ S+NP+ L P A+AARG I G+ SL +G GQFCT Sbjct: 242 AGGRALFDLCAARPEPIPFFGELGSVNPMFLLPEAIAARGAEIGAGWAGSLAMGAGQFCT 301 Query: 305 NPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIGAG 364 NPG+ + + P D F A AL + A MLT+GIA AYR+G +LA P E+ Sbjct: 302 NPGIAVVL--PGADAFVAAAEAALRETAAQTMLTEGIAAAYRDGVARLAAHPQTSELLG- 358 Query: 365 EAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQLTA 424 A +A LY V A+ +LA+ EVFGP L+V +D E+AR+ +L+GQLT Sbjct: 359 -APCDGREAHPCLYRVAARDWLADHTLQEEVFGPLGLVVEAQDAAEMARIARSLQGQLTC 417 Query: 425 TLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTSVGA 484 TL M+ D AR L+P+LERKAGR+LVNG+PTGVEV D+MVHGGP+PA++N TSVG Sbjct: 418 TLHMEDGDTDHARSLVPLLERKAGRMLVNGFPTGVEVADSMVHGGPYPASTNFGATSVGT 477 Query: 485 TAIERFLRPVCYQDFPDDLLP 505 +I RFLRPVCYQ+ PD LLP Sbjct: 478 LSIRRFLRPVCYQNMPDALLP 498 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: 914 Number of extensions: 44 Number of successful extensions: 4 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: 501 Length adjustment: 35 Effective length of query: 490 Effective length of database: 466 Effective search space: 228340 Effective search space used: 228340 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