Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Koxy:BWI76_RS00275 Length = 501 Score = 479 bits (1233), Expect = e-139 Identities = 246/491 (50%), Positives = 339/491 (69%), Gaps = 2/491 (0%) Query: 27 LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86 LL++ + K FPGV ALS L V PG V+AL+GENGAGKST+MK++ GIY DAG L Sbjct: 4 LLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLW 63 Query: 87 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146 GK TF+ P ++ +AGI +IHQELNL+P ++IAENI++GRE +N F ID + M+ Sbjct: 64 LGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206 +LL +L + + ++ VG+LSI ++QMVEIAK +S++S ++IMDEPT A+TD E LF + Sbjct: 124 KLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266 I +LK+QG+GI+YI+H+M E+F I D+V VFRDG +I + S+D D LI MMVGR+L Sbjct: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRKLE 243 Query: 267 QLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGIT 326 +P +K G + + V +L GV + +SF L GEILG+AGLMG+GRT + + ++G Sbjct: 244 DQYPRLDKAPGAVRLKVDNLCGSGV-ENISFILRQGEILGVAGLMGAGRTELMKVLYGAL 302 Query: 327 PSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA-G 385 P G + LDG+ V P + G ++EDRK GL +SV ENM + L +++ G Sbjct: 303 PRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRG 362 Query: 386 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 445 G ++ K + D + VKTPS+EQ I LSGGNQQK +AR LMT P++LILDEP Sbjct: 363 GGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422 Query: 446 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEA 505 TRG+DVGAK EIY+LI+ +EG+++I++SSE+PEVLGMSDR+MVMHEG L G R +A Sbjct: 423 TRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQA 482 Query: 506 TQERVMQLASG 516 TQE +M A G Sbjct: 483 TQEVLMAAAVG 493 Score = 87.8 bits (216), Expect = 8e-22 Identities = 59/227 (25%), Positives = 109/227 (48%), Gaps = 6/227 (2%) Query: 43 LSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQA 102 + ++ +R G +L + G GAG++ LMK++ G +G + L G+ V +P L Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327 Query: 103 GIAMIHQELN---LMPHMSIAENIWIG--REQLNGFHMIDHREMHRCTAQLLERLRINLD 157 GI I ++ L+ MS+ EN+ + R G + H++ + + + + Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGGGSLKHKDEQQAVSDFIRLFNVKTP 387 Query: 158 PEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKG 216 EQ +G LS +Q V IA+ + +LI+DEPT + ++ +I KA+G Sbjct: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEGLS 447 Query: 217 IIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 263 II ++ +M EV ++D + V +G G + + L++ VG+ Sbjct: 448 IILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 494 Lambda K H 0.321 0.137 0.391 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: 664 Number of extensions: 32 Number of successful extensions: 7 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: 521 Length of database: 501 Length adjustment: 35 Effective length of query: 486 Effective length of database: 466 Effective search space: 226476 Effective search space used: 226476 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