Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 469 bits (1208), Expect = e-137 Identities = 242/491 (49%), Positives = 334/491 (68%), Gaps = 2/491 (0%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 LL++ + K FPGV ALS L V PG V+AL+GENGAGKST+MK++ GIY DAG L Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 GK TF P ++ +AGI +IHQELNL+P ++IAENI++GRE +N +D M+ Sbjct: 86 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145 Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 +LL +L ++ ++ VG+LSI ++QMVEIAK +S++S ++IMDEPT A+T+TE LF + Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205 Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243 I +LKSQG+GI+YI+H+M E+F I D+V VFRDG +I + S+ DSLI MMVGR+L Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265 Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302 +P ++ GD+ L V +L G+ VSF L GEILG++GLMG+GRT + + ++G Sbjct: 266 QLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVT 325 Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362 P T G + LDG V P + G ++EDRK GL +SV ENM + L ++ Sbjct: 326 PSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYV-G 384 Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422 G ++ + D + VKTPS+EQ I LSGGNQQK +AR LMT P++LILDEP Sbjct: 385 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEP 444 Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482 TRG+DVGAK EIY+LI+ ++G+++I++SSE+PEVLGMSDR++VMHEG L G R +A Sbjct: 445 TRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLNRGEA 504 Query: 483 TQEVLMAAAVG 493 TQE +M A G Sbjct: 505 TQERVMQLASG 515 Score = 86.3 bits (212), Expect = 2e-21 Identities = 63/232 (27%), Positives = 109/232 (46%), Gaps = 9/232 (3%) Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV +DV +R G +L + G GAG++ LMK++ G +G + L G V +P Sbjct: 37 PGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPL 96 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382 L GI I ++ L+ MS+ EN+ + R + H + + + + Sbjct: 97 AALQAGIAMIHQELN---LMPHMSIAENIWIG--REQLNGLHMVDHGEMHRCTARLLERL 151 Query: 383 NVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFK 442 +K EQ +G LS +Q V IA+ + +LI+DEPT + ++ +I K Sbjct: 152 RIKLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSIIADLK 210 Query: 443 ADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 + G II ++ +M EV ++D + V +G G + + L++ VG+ Sbjct: 211 SQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGR 262 Lambda K H 0.318 0.137 0.380 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: 662 Number of extensions: 34 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: 501 Length of database: 517 Length adjustment: 34 Effective length of query: 467 Effective length of database: 483 Effective search space: 225561 Effective search space used: 225561 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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