Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate H281DRAFT_03878 H281DRAFT_03878 xylose ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Burk376:H281DRAFT_03878 Length = 519 Score = 430 bits (1106), Expect = e-125 Identities = 232/506 (45%), Positives = 334/506 (66%), Gaps = 13/506 (2%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPD--YEGQI 69 LL R I K F GV A++ + L + GE L GENGAGKSTLMK+L+GVYP ++G+I Sbjct: 5 LLTMRGIVKAFSGVKALDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEI 64 Query: 70 FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129 EGK ++ + R+ + GI +I QEL LVP LS AENIFL E G + Y M+++ Sbjct: 65 TWEGKPLKATSIRDTERAGIIIIHQELMLVPELSVAENIFLGNEITLPGGRMNYAAMYQR 124 Query: 130 ASKLFSKLGVN-IDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQL 188 A +L +LG++ I+ V + QQ++ IAKAL+ AK++I+DEP+S++ E L Sbjct: 125 ADELLRELGISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAIL 184 Query: 189 FNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGR 248 +I+R LK G + +YISH+L+E+ + D + V+RDGR V P+ D+++ LMVGR Sbjct: 185 LDIVRDLKRRGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGR 244 Query: 249 SIDQFFIKERATITDEIFRVEGIKLWSLDR-KKLLVDDVSFYVRKGEVLGIYGLVGAGRT 307 I F +E I D IF + + + ++ V DVSF +R+GE+LG+ GLVGAGRT Sbjct: 245 EIKNLFPREPHPIGDVIFEARNVTCFDVTNPRRKRVSDVSFELRRGEILGVAGLVGAGRT 304 Query: 308 ELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNI 367 EL++AIFGA+PG +E V + GK +KI +P DA++ GIG+VPEDRK G++ +SV HNI Sbjct: 305 ELMQAIFGAYPGVSEATVVMEGKTVKIRAPIDAIRAGIGMVPEDRKRHGIVPGLSVGHNI 364 Query: 368 TLPSVVMKLIVRKF---GLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVL 424 TL ++++F G IDS E + + + +++L+++ P + +LSGGNQQK VL Sbjct: 365 TLA------VLQRFSSGGRIDSAAELDTIHTEMKRLSVRAAHPMLSIASLSGGNQQKAVL 418 Query: 425 AKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRIL 484 + L PKVL+LDEPTRG+DV AK EIYKLI ++A GM +VMVSSELPE+L +SDR+L Sbjct: 419 TRMLLTDPKVLILDEPTRGVDVGAKFEIYKLIFQLAQRGMSIVMVSSELPEVLGISDRVL 478 Query: 485 VMSEGRKTAEFLREEVTEEDLLKAAI 510 V+ EG +F+ + +T+ED+L AAI Sbjct: 479 VIGEGELRGDFVNDGLTQEDILSAAI 504 Score = 91.7 bits (226), Expect = 6e-23 Identities = 65/234 (27%), Positives = 121/234 (51%), Gaps = 8/234 (3%) Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHP-GRTEGKVFIGGKEIKIHSPRDAV 341 +D + V GE +G+ G GAG++ L++ + G +P G +G++ GK +K S RD Sbjct: 21 LDGIDLTVSPGECVGLCGENGAGKSTLMKVLSGVYPHGTWDGEITWEGKPLKATSIRDTE 80 Query: 342 KNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLN 401 + GI ++ ++ L+ ++SV NI L + + R Q E++R +L Sbjct: 81 RAGIIIIHQELM---LVPELSVAENIFLGNEITLPGGRMNYAAMYQRADELLR----ELG 133 Query: 402 IKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAV 461 I + Q V N GG+QQ + +AK L + K+L+LDEP+ + + + + ++ ++ Sbjct: 134 ISGINAAQPVMNYGGGHQQLIEIAKALNKQAKLLILDEPSSSLTSSEIAILLDIVRDLKR 193 Query: 462 SGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515 G+ V +S +L E+ A+ D I V+ +GR A +T + ++ + R +K Sbjct: 194 RGVACVYISHKLDEVAAVCDTISVIRDGRHVATEPMHALTTDRIISLMVGREIK 247 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: 622 Number of extensions: 39 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: 519 Length adjustment: 35 Effective length of query: 488 Effective length of database: 484 Effective search space: 236192 Effective search space used: 236192 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