Align Inositol transport system ATP-binding protein (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 303 bits (777), Expect = 8e-87 Identities = 182/504 (36%), Positives = 288/504 (57%), Gaps = 17/504 (3%) Query: 24 LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83 +E+ ISK F V A D+ +RV PGT+ ++GENGAGKSTLM I+ G Y+ DAGEI ++ Sbjct: 26 IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIK 85 Query: 84 GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143 G+ AA +AGI M+ Q L+ + ++ EN+ +G E+ +L + + + E Sbjct: 86 GQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEE-GALLRPSLAKARKLLRE 144 Query: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203 L +N+ P+ + +LS+ +Q VEI KA+ +DILI+DEPT +T E HLF I+ Sbjct: 145 LSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRIL 204 Query: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQ 263 LK++GK I+ ITHK+ E+ D V+V R G + + + L +MVGR++ Sbjct: 205 EGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVGRKV-- 262 Query: 264 LFPLRETPI--GDLLLTVRDLTL---DGV--FKDVSFDLHAGEILGIAGLMGSGRTNVAE 316 L + +TP G +LTV DL + GV K +S + AGE+LGIAG+ G+G++ + E Sbjct: 263 LLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSELLE 322 Query: 317 TIFGITPSSSGQITLDGKAVRISDPHMAIE----KGFALLTEDRKLSGLFPCLSVLENME 372 + G+ P++ G++T+ G+ + ++ H + +G A + EDR+ GL EN+ Sbjct: 323 VLGGMRPAT-GRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWENVA 381 Query: 373 MAVL--PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 430 P Y + +A+RA E + V+ SGGNQQK +LAR + Sbjct: 382 FGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLAREIE 441 Query: 431 TNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEG 490 NP LL++ +PTRG+D+GA I++ I L G A++++S EL E+L +SDRV VM +G Sbjct: 442 RNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMFDG 501 Query: 491 ELMGTLDRSEATQEKVMQLASGMT 514 +MG +E ++++ L +G+T Sbjct: 502 RIMGERPAAETNEKELGLLMAGIT 525 Lambda K H 0.320 0.136 0.381 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: 649 Number of extensions: 29 Number of successful extensions: 7 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: 517 Length of database: 548 Length adjustment: 35 Effective length of query: 482 Effective length of database: 513 Effective search space: 247266 Effective search space used: 247266 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