Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Pf6N2E2_1456 D-xylose transport ATP-binding protein XylG
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1456 Length = 518 Score = 402 bits (1034), Expect = e-116 Identities = 214/505 (42%), Positives = 327/505 (64%), Gaps = 7/505 (1%) Query: 10 EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEG 67 + LL+ I KTF GV A+N + +++ GE L GENGAGKSTLMK+L+ VYP ++G Sbjct: 3 DYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDG 62 Query: 68 QIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMF 127 +I +G+ ++ ++ E + GI +I QEL LVP+LS AENIF+ E G + Y M Sbjct: 63 EILWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPAMI 122 Query: 128 EQASKLFSKLGV-NIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETE 186 +A L +L V +++ V QQ+V IAKAL+ A+++I+DEP+SA+ + E E Sbjct: 123 HRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIE 182 Query: 187 QLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMV 246 L +IIR LK +G + +YISH+L+E+ + D + V+RDG+ + + + K++ MV Sbjct: 183 VLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMV 242 Query: 247 GRSIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAG 305 GR + + E + + IF + +D ++ VDD+SF +++GE+LGI GLVGAG Sbjct: 243 GREMSNLYPTEPHDVGEVIFEARHFTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVGAG 302 Query: 306 RTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLH 365 RTEL+ A+FGA+PGR EG+V++ G++I +P +++ G+ +VPEDRK G+I + V Sbjct: 303 RTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGVGQ 362 Query: 366 NITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLA 425 NITL + K ID++ E + I ++++KT SP+ + +LSGGNQQK VLA Sbjct: 363 NITLAVLDN---YSKLTRIDAEAELGSIDKEISRMHLKTASPFLPITSLSGGNQQKAVLA 419 Query: 426 KWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILV 485 K L KP+VL+LDEPTRG+DV AK EIYKL+ +A G+ ++MVSSEL E+L +SDR+LV Sbjct: 420 KMLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLV 479 Query: 486 MSEGRKTAEFLREEVTEEDLLKAAI 510 + +G+ +F+ E+T+E +L AA+ Sbjct: 480 IGDGQLRGDFINHELTQEQVLAAAL 504 Score = 73.9 bits (180), Expect = 1e-17 Identities = 57/239 (23%), Positives = 114/239 (47%), Gaps = 20/239 (8%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341 ++ + VR GE +G+ G GAG++ L++ + +P G +G++ G+ +K S + Sbjct: 21 LNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPYGTWDGEILWDGQPLKAQSISETE 80 Query: 342 KNGIGLVPEDRKTAGLILQMSVLHNI------TLPSVVMKLIVRKFGLIDSQLEKEIVRS 395 GI ++ ++ L+ +SV NI TLP M + + + E + Sbjct: 81 AAGIVIIHQELT---LVPDLSVAENIFMGHELTLPGGRMN-----YPAMIHRAEALMREL 132 Query: 396 FIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKL 455 + +N+ P V GG QQ V +AK L + ++L+LDEP+ + + + + Sbjct: 133 KVPDMNVSLP-----VSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSEIEVLLDI 187 Query: 456 ISEMAVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSV 514 I ++ G+ V +S +L E+ A+ D I V+ +G+ A +++ ++ + R + Sbjct: 188 IRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMADMSIPKIITQMVGREM 246 Lambda K H 0.317 0.137 0.372 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: 637 Number of extensions: 26 Number of successful extensions: 9 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: 523 Length of database: 518 Length adjustment: 35 Effective length of query: 488 Effective length of database: 483 Effective search space: 235704 Effective search space used: 235704 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 (21.6 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