Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 257 bits (657), Expect = 6e-73 Identities = 163/486 (33%), Positives = 263/486 (54%), Gaps = 21/486 (4%) Query: 3 ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62 A LQL GI K +PG A L++ PG + AL+GENGAGKST+MK++ G+ DAG + Sbjct: 7 ARLQLCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIH 66 Query: 63 WLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122 W G+ T P ++E GIG++ Q +L L++AENI L + G K + + Sbjct: 67 WQGERVTMRDPAQARERGIGMVFQHFSLFETLSVAENIALA--LGAKAGTP--KQLEPKI 122 Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 ++ + + + +LV LSIG++Q VEI + L + +++I+DEPT LT E + LF Sbjct: 123 REVSQRYGMPLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 182 Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG--R 240 +R L ++G I++ISH++ E+ +C TV R G+ E A ++ L +MVG Sbjct: 183 TLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAE 242 Query: 241 KLEDQYPHLD-KAPGDIRLKVDNLC-------GPGVNDVSFTLRKGEILGVSGLMGAGRT 292 LE +YP + +AP L+V+ L G + +V +R GEI+G++G+ G G+ Sbjct: 243 GLEAEYPKSEGRAP---FLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQD 299 Query: 293 ELMKVLYGALPRTSGY---VTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349 EL+ +L G + + G +V P +G+ ++ +R G V MS+ + Sbjct: 300 ELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLAD 359 Query: 350 NMSLTALRYFSRA-GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIAR 408 N LTA + G ++ + I+ F VKTP + LSGGN QK + R Sbjct: 360 NGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGR 419 Query: 409 GLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVM 468 ++ +PK+LI PT GVDVGA I++ + + + G +I+++S ++ E+ +SDRI + Sbjct: 420 EILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAAL 479 Query: 469 HEGHLS 474 +G LS Sbjct: 480 SDGRLS 485 Score = 82.0 bits (201), Expect = 5e-20 Identities = 70/247 (28%), Positives = 114/247 (46%), Gaps = 18/247 (7%) Query: 263 LCG-----PG--VND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGH 314 LCG PG ND + +++ GEI + G GAG++ LMK++YG +G + G Sbjct: 11 LCGITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGE 70 Query: 315 EVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQA 374 V R P GI + + L +SV EN+ AL ++AG + + + Sbjct: 71 RVTMRDPAQARERGIGMVFQ---HFSLFETLSVAENI---ALALGAKAGTPKQLEPKIRE 124 Query: 375 VSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEI 434 VS + ++ + LS G +Q+V I R LM ++LILDEPT + E+ Sbjct: 125 VSQRYGM----PLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADEL 180 Query: 435 YQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 + + + A+G SI+ +S ++ EV + V+ G +SGE + + L VG Sbjct: 181 FVTLRRLAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGD 240 Query: 495 LNRVNQE 501 + E Sbjct: 241 AEGLEAE 247 Score = 58.2 bits (139), Expect = 7e-13 Identities = 49/232 (21%), Positives = 104/232 (44%), Gaps = 10/232 (4%) Query: 19 ALSGAALNVYPGRVMALVGENGAGKSTMMKVLTG---IYTRDAGTLLWLGKETTFTGPKS 75 +L L V G ++ + G G G+ ++ +L+G + A + +LG + P + Sbjct: 274 SLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGA 333 Query: 76 SQEAGIGIIHQEL---NLIPQLTIAENIFLG---REFVNRFGKIDWKTMYAEADKLLAKL 129 + G+ + E +P +++A+N L + + G I + A A++++ + Sbjct: 334 RRRHGMAFVPAERLGHGAVPSMSLADNGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRF 393 Query: 130 NLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELK 188 ++ + LS G+ Q + + + + K++I PT + ++ R + EL+ Sbjct: 394 AVKTPDAQTPAASLSGGNLQKFILGREILQQPKLLIAAHPTWGVDVGAAAAIHRALIELR 453 Query: 189 SQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240 G I+ IS ++E+F+I D + DG+ +R AS + M G+ Sbjct: 454 DAGAAILVISEDLEELFQISDRIAALSDGRLSPQRATASTCPVEVGRWMAGQ 505 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: 564 Number of extensions: 27 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 501 Length of database: 518 Length adjustment: 34 Effective length of query: 467 Effective length of database: 484 Effective search space: 226028 Effective search space used: 226028 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