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 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 237 bits (605), Expect = 7e-67 Identities = 150/472 (31%), Positives = 251/472 (53%), Gaps = 12/472 (2%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +++ E + K++ V A D L + G + AL G NGAGKST +SIL G +D G I + Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 +G V+F P +AL AGI M+ Q + MTVAEN+ LG+ +G + ++R Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQ----SGAWLSPVHMSRVVA 149 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 EL D+D + + LS+ + Q VEI K D +V+I+DEPT+ + E + LF+A Sbjct: 150 ELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEA 209 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRD-HLVRGIVGQEL 244 + R+ G IV++SH++ E+ +AD+ +I R G V+ +++ + L +VG+E+ Sbjct: 210 LHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREV 269 Query: 245 TRIDHKVGRECA--ANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCI 302 +V E + L VD L+ G +S ++R+GE+ I G+ G+G+ E + C+ Sbjct: 270 IL---EVAAEPLEPGDRVLHVDGLAGDG-LKGLSFEVRKGEVFAIAGVAGNGQRELVECV 325 Query: 303 YGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKR 362 GL G V L G P KA G++ + EDR+ L+ ++ N L+A Sbjct: 326 TGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARGC 385 Query: 363 LSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLC 422 + ++ + A D++ ++ E P S+SGGN QK+V+ + +P ++ Sbjct: 386 FTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVA 445 Query: 423 DEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGG 474 + PT+G+D A +E++ L + VR ++VS + E+L L+DR+AV G Sbjct: 446 ENPTQGLDIAATEEVWARLLE-VRSHAGVLLVSGDLNEVLALADRVAVMYRG 496 Score = 76.6 bits (187), Expect = 2e-18 Identities = 53/219 (24%), Positives = 106/219 (48%), Gaps = 9/219 (4%) Query: 273 HDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAG 332 HDI+L + G I + G G+G+S ++ + G D+G + + G+ + PK + AG Sbjct: 51 HDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAG 110 Query: 333 MSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKRLQIKTTSL 392 + +V + LV + ++ N+ L S + ++ +++ ++ R + Sbjct: 111 IGMVYQHFM---LVDSMTVAENVLLG-----QSGAWLSPVHMSRVVAELAARYGLDIDPA 162 Query: 393 ELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAI 452 V +S G +Q+V + K L + L+ DEPT + G ++++ L + G A + Sbjct: 163 AR-VCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIV 221 Query: 453 VVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALL 491 +S + E+L L+D IA+ + G +V ++ + EA L Sbjct: 222 FISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAEL 260 Score = 50.1 bits (118), Expect = 2e-10 Identities = 43/201 (21%), Positives = 91/201 (45%), Gaps = 10/201 (4%) Query: 29 LRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGIAMITQ 88 +R G V A+ G G G+ + + G+ + G + L G P + G+A I + Sbjct: 302 VRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPE 361 Query: 89 ELEPIPY---MTVAENIWL-GREPRRAGCIVDNKALNRRTRELLDSLEFDVD---ATSPM 141 + + + + + +N L R G +D K+ + R++L E++V A +P Sbjct: 362 DRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDIL--AEYNVQPGRAEAPA 419 Query: 142 HRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVYVSH 201 LS +Q + + + F +++ + PT + + ++ + + + AG++ VS Sbjct: 420 RSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSH-AGVLLVSG 478 Query: 202 RLSELAQIADDYSIFRDGAFV 222 L+E+ +AD ++ G F+ Sbjct: 479 DLNEVLALADRVAVMYRGCFI 499 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: 592 Number of extensions: 33 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: 495 Length of database: 524 Length adjustment: 34 Effective length of query: 461 Effective length of database: 490 Effective search space: 225890 Effective search space used: 225890 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 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