Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 473 bits (1216), Expect = e-138 Identities = 244/491 (49%), Positives = 336/491 (68%), Gaps = 2/491 (0%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 LL++ I K FPGV AL+ L V PG V+AL+GENGAGKST+MK++ GIY DAG + Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 GK F P ++Q+AGI +IHQELNL+P ++IAENI++GRE +N ++ + M+ Sbjct: 83 RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142 Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 +LLA+L + ++ VG+LSI ++QMVEIAK +S++S ++IMDEPT A+T+ E LF + Sbjct: 143 ELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSI 202 Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243 I +LKSQG+GIVYI+H+M E+F I D+V VFRDG +I + S+ DSLI MMVGR+L Sbjct: 203 IADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELS 262 Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302 +P + GD+ L V +L GV DVSF L GEILG++GLMG+GRT + + ++G Sbjct: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322 Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362 P +SG +TLDG V P + G ++EDRK GL +SV ENM + L +++ Sbjct: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYT-G 381 Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422 G ++ + D + VKTPS+EQ I LSGGNQQK +AR LMT P++LILDEP Sbjct: 382 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441 Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482 TRG+DVGAK EIY+LI ++G+++I++SSE+PEVLGMSDR++VMHEG L G R +A Sbjct: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501 Query: 483 TQEVLMAAAVG 493 TQE +M A G Sbjct: 502 TQEKVMQLASG 512 Score = 89.4 bits (220), Expect = 3e-22 Identities = 61/232 (26%), Positives = 110/232 (47%), Gaps = 9/232 (3%) Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV DV +R G +L + G GAG++ LMK++ G +G + L G +V +P Sbjct: 34 PGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPL 93 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382 GI I ++ L+ MS+ EN+ + + S + H + + ++ + Sbjct: 94 AAQKAGIAMIHQELN---LMPHMSIAENIWIGREQLNSLH--MVNHREMHRCTAELLARL 148 Query: 383 NVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFK 442 + EQ +G LS +Q V IA+ + +LI+DEPT + ++ +I K Sbjct: 149 RINLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLK 207 Query: 443 ADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 + G I+ ++ +M EV ++D + V +GH G + + L++ VG+ Sbjct: 208 SQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGR 259 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: 619 Number of extensions: 31 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 Apr 09 2024. 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