Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BPHYT_RS28455 BPHYT_RS28455 2,5-dioxovalerate dehydrogenase
Query= reanno::HerbieS:HSERO_RS00735 (529 letters) >FitnessBrowser__BFirm:BPHYT_RS28455 Length = 533 Score = 709 bits (1831), Expect = 0.0 Identities = 363/524 (69%), Positives = 423/524 (80%), Gaps = 1/524 (0%) Query: 5 ILGHNYIGGQRSGQGDVALHSVDATTGALFETPFLTATDKEVAAAVHAAEQAYPLYRATT 64 I GHNYIGGQRS GD++LHS+ A+T ++ F ATD EV AAV AA A+PLYRA Sbjct: 5 IFGHNYIGGQRSACGDISLHSLSASTSEVYPVAFSQATDAEVDAAVEAAAAAFPLYRALP 64 Query: 65 SEQRAQFLEAIADEIDALGDDFLAAVARETALPATPRLAGERARTSGQMRLFAKVVRRGD 124 S RA FLEAIA EIDALGDDF+A V RETALP R+AGERARTS QMRLFAKV+RRGD Sbjct: 65 SSVRADFLEAIAAEIDALGDDFIADVMRETALP-NARIAGERARTSNQMRLFAKVLRRGD 123 Query: 125 FYGARIDTALPQRQPLPRPDIRQYKIGVGPVAVFGASNFPLAFSVAGGDTAAALAAGCPV 184 FYGARID ALP+RQPLPRPD+RQY+IGVGPVAVFGASNFPLAFSVAGGDTA+ALAAGCPV Sbjct: 124 FYGARIDRALPERQPLPRPDLRQYRIGVGPVAVFGASNFPLAFSVAGGDTASALAAGCPV 183 Query: 185 VFKAHSGHLVTSELVADAIERAVKKTGMPAGTFNMIYGDRVGAQLVKSAGIQAVGFTGSL 244 V KAHSGHLVTSE +ADAIERA+++TGMPAGTFNMIYG+RVGA+LV++ GIQAVGFTGSL Sbjct: 184 VVKAHSGHLVTSERMADAIERAIRRTGMPAGTFNMIYGERVGARLVQAPGIQAVGFTGSL 243 Query: 245 RGGRALCDMAAARPQPIPVFAEMSSINPIILMPEALKLRGDAIAKDLAGSVTVGVGQLCT 304 GGRALCD+AAAR QPIPVFAEMSS+NP+ ++ AL+ RG A+A +LA SV G GQLCT Sbjct: 244 SGGRALCDLAAAREQPIPVFAEMSSVNPVFVLEGALQERGAALANELAASVATGCGQLCT 303 Query: 305 SPGLLLGVRSPELTSFIEKLSAAFGGTNPATMLNSGGLTHYNGGVARLTQLPGVKVIATG 364 SPGL+LGVRSP +FI+ L A P TMLN+G ++ G+ R + G+ + A Sbjct: 304 SPGLVLGVRSPRFGAFIDSLGKAIERQPPQTMLNTGIFANFRAGLERASNHAGIALSAAA 363 Query: 365 GTSYTQAVPHLFKADAALLFSKEAPLEEEVFGPSTVIVELESREQLLDFAAKMNGQLTAT 424 QA LF ADAALLF PLEEE+FGP+TV+VEL+S E LL FA+ M GQLTAT Sbjct: 364 QGETEQAAAQLFVADAALLFDPGRPLEEEIFGPATVVVELDSAEHLLRFASAMRGQLTAT 423 Query: 425 LQAEIGDLQGNQDLIAILEQKAGRLLLNGFPTGVEVCDAMVHGGPYPATSDARGTSVGSL 484 L A GDL+ ++ LI LE+KAGRLL+NG+PTGVEV DA+VHGGP+PATSDARGTSVG+L Sbjct: 424 LLASHGDLRSHRKLIERLEEKAGRLLVNGYPTGVEVSDAIVHGGPWPATSDARGTSVGTL 483 Query: 485 AIERFLRPVCYQNYPDAMLPAALQNANPLGLMRLVDGEQTRATV 528 AI+RFLRPVCYQNYPD +LP AL+NANPL LMRLVDGE T+ ++ Sbjct: 484 AIDRFLRPVCYQNYPDELLPDALKNANPLNLMRLVDGEMTQRSL 527 Lambda K H 0.318 0.135 0.387 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: 38 Number of successful extensions: 2 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: 529 Length of database: 533 Length adjustment: 35 Effective length of query: 494 Effective length of database: 498 Effective search space: 246012 Effective search space used: 246012 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 (21.7 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