Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate SM_b20262 SM_b20262 semialdehyde dehydrogenase
Query= SwissProt::Q08IC0 (525 letters) >FitnessBrowser__Smeli:SM_b20262 Length = 505 Score = 499 bits (1285), Expect = e-146 Identities = 270/502 (53%), Positives = 331/502 (65%), Gaps = 7/502 (1%) Query: 5 GEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQPL 64 G+ L+ E + G AGT A P+ G D F V V RACE A +AF Y Sbjct: 7 GKHLVAGEWLDG-AGTF-ASAPAHGPAHD---FAVGTVELVNRACEAAEEAFWTYGYSSR 61 Query: 65 AARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGRFL 124 RAAFL AIADEI A +A+ E ETGLP ARL GERGRT GQLRLFA + G +L Sbjct: 62 KERAAFLRAIADEIEARAEAITEIGSQETGLPEARLNGERGRTTGQLRLFADHIEKGDYL 121 Query: 125 AASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPVIV 184 +D A P R P PR ++RL + +GPV VFGASNFPLAFS AGGDTA+ALAAGCPV+V Sbjct: 122 DRRVDAAMPERQPAPRQEIRLVQRPVGPVAVFGASNFPLAFSTAGGDTAAALAAGCPVVV 181 Query: 185 KAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTGSR 244 K H AH GT E+V A+ AA+ KTG+ GVFSL+ G R +G ALV HP ++AVGFTGS Sbjct: 182 KGHSAHPGTGEIVAEAVDAAIRKTGVHPGVFSLIQGGSRDVGHALVQHPHIKAVGFTGSL 241 Query: 245 QGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQFCT 304 GG AL + ARP+PIP + E+ S+NP+ L P AL AR + + G+ SLT+G GQFCT Sbjct: 242 AGGRALFDLCAARPEPIPFFGELGSVNPMFLLPEALKARAETLGQGWAGSLTMGAGQFCT 301 Query: 305 NPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIGAG 364 NPG+ + I+G D DRF T A +ALAK MLT GIA AYR+G+ + A V+ + A Sbjct: 302 NPGIAVVIEGADADRFTTAAVEALAKVAPQTMLTDGIAKAYRDGQARFATRNAVKPLLAT 361 Query: 365 EAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQLTA 424 E++ D A L+E FLA+ A EVFGP L+VR E+ + +GQLTA Sbjct: 362 ESSGRD--ASPNLFETTGAQFLADHALGEEVFGPLGLVVRVGSPAEMEELARGFQGQLTA 419 Query: 425 TLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTSVGA 484 T+ MDA D ARRL PVLERKAGR+LVNG+PTGVEV D+MVHGGP+PA++N TSVG Sbjct: 420 TIHMDAGDLETARRLRPVLERKAGRVLVNGFPTGVEVVDSMVHGGPYPASTNFGATSVGT 479 Query: 485 TAIERFLRPVCYQDFPDDLLPE 506 +I RFLRPV YQ+ P+DLLPE Sbjct: 480 MSIRRFLRPVAYQNMPEDLLPE 501 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: 850 Number of extensions: 42 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: 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 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