Align Inositol transport system ATP-binding protein (characterized)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 429 bits (1104), Expect = e-125 Identities = 222/496 (44%), Positives = 328/496 (66%), Gaps = 8/496 (1%) Query: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 +L + NI+K F GV AL DV L ++ G V A++GENGAGKSTLMKI++G+Y G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 G P+ F+ AQ+ GI +IHQELNL+P++SI ENI++GRE + +++ +MH+ A Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA 120 Query: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 +LL RL++N+DPE V L + ++Q+VEIAKA+S +S ++IMDEPTSAI+++EV LF I Sbjct: 121 QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI 180 Query: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 I L+++GK I YI+HK++E+FAIAD V RDG I + M ++LI MVGRE+ Sbjct: 181 IRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIV 240 Query: 263 QLFPLRETPIGDLLLTVRDLTLDG-------VFKDVSFDLHAGEILGIAGLMGSGRTNVA 315 + +L+V+ LT+ + +D++F+L GE+LGI GLMG+GRT + Sbjct: 241 IERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELM 300 Query: 316 ETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 375 E +FG+ P +ITL GK P A++ G AL+ EDRK GL C+ + N + V Sbjct: 301 EALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTV 360 Query: 376 LPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRL 435 + G + K + L + +L++K S Q ++ LSGGNQQK +LA+WL T P++ Sbjct: 361 VDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPKV 420 Query: 436 LILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGT 495 L+LDEPTRGID+ AK EIY+LI LA+EG+ +I++SSELPE+L +SDRV+VM EG L Sbjct: 421 LMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTAN 480 Query: 496 LD-RSEATQEKVMQLA 510 + ++ ++++++Q A Sbjct: 481 IPIDAQTSEDEILQAA 496 Score = 96.7 bits (239), Expect = 2e-24 Identities = 66/245 (26%), Positives = 123/245 (50%), Gaps = 9/245 (3%) Query: 276 LLTVRDLTLDGV----FKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITL 331 +LTV+++T + V DVS +L AG + I G G+G++ + + + G+ P G I Sbjct: 1 MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60 Query: 332 DGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALR 391 +G V+ + A EKG ++ ++ L P LS+ EN+ + P T G + + Sbjct: 61 NGDPVKFQNTRDAQEKGINIIHQELNL---IPYLSIRENIFLGREPE-TPMGLLDVAKMH 116 Query: 392 ALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKA 451 + +L++ E + L G QQ +A+ L +++I+DEPT I Sbjct: 117 KEAAQLLHRLKLNVDP-ETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVE 175 Query: 452 EIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLAS 511 ++ +I L +EG A+ IS +L E+ ++DR +V+ +G+++ + + T+E ++Q Sbjct: 176 ILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235 Query: 512 GMTAV 516 G V Sbjct: 236 GREIV 240 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: 603 Number of extensions: 29 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 502 Length adjustment: 34 Effective length of query: 483 Effective length of database: 468 Effective search space: 226044 Effective search space used: 226044 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