Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate SMc02325 SMc02325 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Smeli:SMc02325 Length = 503 Score = 439 bits (1130), Expect = e-128 Identities = 229/494 (46%), Positives = 328/494 (66%), Gaps = 2/494 (0%) Query: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 M+ + L+GI K+FPGV+ALS +L +YPG V ALVGENGAGKST++K+LTGIY DAGT Sbjct: 1 MKPAIALEGISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGT 60 Query: 61 LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 + ETTF ++ AG+ IHQE L +L++AENIFLG NRFG IDWK + A Sbjct: 61 IRLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNA 120 Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 +A LL + F + DL I + +V IA+ LS +++V+IMDEPT AL+ E L Sbjct: 121 DAQALLGRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHEL 180 Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240 + +I LK+ G+ +++ISH+ EIF I D TVFRDG I E +A +++D L+ MMVGR Sbjct: 181 YDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGR 240 Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGP-GVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299 + YP + G L V P D++F LR+GEILG GL+GAGR+E M+ L Sbjct: 241 AVGSVYPKKEVTIGQPVLTVSGYRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLI 300 Query: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359 G ++G V LDG +V RSP + + GIVY+ E+R R G ++GM + +N++L +L + Sbjct: 301 GITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHT 360 Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419 SR+ G L+ A+E ++ +++ +++Q +G LSGGNQQKV IA+ L TRPKV+IL Sbjct: 361 SRS-GFLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIIL 419 Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479 DEPT+G+D+G+K ++ +++ A GLS+I+VSSE+PE++GMSDR+IVM EG ++G + R Sbjct: 420 DEPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYER 479 Query: 480 EQATQEVLMAAAVG 493 + T E L+ AA G Sbjct: 480 SELTAEKLVRAAAG 493 Score = 80.1 bits (196), Expect = 2e-19 Identities = 69/234 (29%), Positives = 109/234 (46%), Gaps = 13/234 (5%) Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV +DVS L G + + G GAG++ L+K+L G +G + L E + Sbjct: 15 PGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRLGDTETTFPTAL 74 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382 G+ I ++ L +SV EN+ L + R L D +Q +D L Sbjct: 75 AASRAGVTAIHQETV---LFDELSVAENIFLG---HAPRNRFGL--IDWKQLNADAQALL 126 Query: 383 NVKTPSMEQAIGLLSGGNQQK--VAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440 + I L G +K VAIAR L +V+I+DEPT + E+Y LI + Sbjct: 127 GRAGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIER 186 Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 KADG +++ +S + E+ ++DR V +G + GE +Q+ L+ VG+ Sbjct: 187 LKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGR 240 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: 674 Number of extensions: 28 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: 501 Length of database: 503 Length adjustment: 34 Effective length of query: 467 Effective length of database: 469 Effective search space: 219023 Effective search space used: 219023 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