Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_01223 H281DRAFT_01223 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_01223 Length = 509 Score = 360 bits (925), Expect = e-104 Identities = 206/481 (42%), Positives = 290/481 (60%), Gaps = 4/481 (0%) Query: 7 LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66 L+ H +K++ V AL DG LSL G VHAL G NGAGKST + IL G+ Q D+G +L++ Sbjct: 11 LELRHASKSFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLVKILAGVHQPDSGELLVD 70 Query: 67 GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126 G +F P++A AG+A+I QE +++AENI++GR+P + A+ R Sbjct: 71 GVARRFATPAQARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRFGRIQYDAMRREVDG 130 Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186 LL SL D+ A + LS+A Q++EIAKA S + V+IMDEPT+A+ E + LF + Sbjct: 131 LLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLTEVERLFAIV 190 Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTR 246 R+L + I++++HRL E+ + +I RDGA V G AD++ D +V +VG++L Sbjct: 191 RKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTADLNTDAIVSKMVGRDLET 250 Query: 247 IDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLT 306 K R L V L+R G F DIS +R GEI+ + GL+G+GRSE I+G+ Sbjct: 251 FYPKAERP-PGEARLSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGID 309 Query: 307 VADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSW 366 D+G + + GKP+ G P A + AG++LV EDR+ GL L SI N +++ RL Sbjct: 310 PLDAGQIQIGGKPLADGSPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVRH 369 Query: 367 SLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPT 426 LI R ETQLA RL++K PV +SGGNQQKVVL K L+T P L+ DEPT Sbjct: 370 GLITTRSETQLANQWGTRLRLKAGDPNAPVGMLSGGNQQKVVLGKWLATNPKVLIIDEPT 429 Query: 427 RGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALS 486 RGID GAK E+Y L + VR G A +++SSE PE+L ++DR+ V GR IS D A + Sbjct: 430 RGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGR---ISADIARA 486 Query: 487 Q 487 + Sbjct: 487 E 487 Score = 79.7 bits (195), Expect = 2e-19 Identities = 59/233 (25%), Positives = 106/233 (45%), Gaps = 9/233 (3%) Query: 19 VPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEA 78 V +D +RAG + AL G GAG+S + GI DAG I + G P+ P+ A Sbjct: 272 VGVFKDISFDVRAGEIVALAGLVGAGRSEVARAIFGIDPLDAGQIQIGGKPLADGSPAAA 331 Query: 79 LAAGIAMITQELEPIPY---MTVAENIW---LGREPRRAGCIVDNKALNRRTRELLDSLE 132 + AG+A++ ++ +++A N LGR R ++ ++ + + L Sbjct: 332 VRAGLALVPEDRRQQGLALELSIARNASMTVLGRLVRHG--LITTRSETQLANQWGTRLR 389 Query: 133 FDV-DATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTA 191 D +P+ LS Q V + K + + +V+I+DEPT I ++ A+ L Sbjct: 390 LKAGDPNAPVGMLSGGNQQKVVLGKWLATNPKVLIIDEPTRGIDVGAKAEVYSALAELVR 449 Query: 192 QGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244 G ++ +S L E+ +AD + +G A+ D + ++ +GQ + Sbjct: 450 DGMAVLMISSELPEVLGMADRVLVMHEGRISADIARAEADEERIMAAALGQPI 502 Score = 56.6 bits (135), Expect = 2e-12 Identities = 47/227 (20%), Positives = 99/227 (43%), Gaps = 5/227 (2%) Query: 265 NLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGL 324 + R D L L GE+ + G G+G+S + + G+ DSG + + G Sbjct: 19 SFGRVRALSDGDLSLWPGEVHALLGENGAGKSTLVKILAGVHQPDSGELLVDGVARRFAT 78 Query: 325 PKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKR 384 P +AG++++ ++ L SI NI + + + + I + + ++ Sbjct: 79 PAQARDAGLAVIYQEPT---LFFDLSIAENIFMGR-QPVDRFGRIQYDAMRREVDGLLAS 134 Query: 385 LQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQF 444 L + + +L V +S +QQ + +AK LS L+ DEPT + + ++ ++ + Sbjct: 135 LGVDLRADQL-VRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLTEVERLFAIVRKL 193 Query: 445 VRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALL 491 A + ++ E+ L+ R+ + + G V L+ +A++ Sbjct: 194 RERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGMTADLNTDAIV 240 Lambda K H 0.319 0.135 0.381 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: 606 Number of extensions: 30 Number of successful extensions: 6 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: 495 Length of database: 509 Length adjustment: 34 Effective length of query: 461 Effective length of database: 475 Effective search space: 218975 Effective search space used: 218975 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