Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 263 bits (673), Expect = 9e-75 Identities = 167/493 (33%), Positives = 266/493 (53%), Gaps = 18/493 (3%) Query: 20 VPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDI 79 +P + LR + KR+PG LA D +A GE+HAL+GENGAGKSTLMKI+ GV DSG++ Sbjct: 11 IPRLQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEM 70 Query: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI-DEDELN 138 + G+ V + P QA+ LGIG++ Q +L LS AQNI + AMG +L Sbjct: 71 IWQGQRVTMRNPAQARGLGIGMVFQHFSLFETLSVAQNIAL------AMGAAAGTPKQLE 124 Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198 + + R + ++P V L++ +Q VEI + L D R+LI+DEPT+ L E E Sbjct: 125 PKIREVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADE 184 Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258 LF +R L A+G I++ISHK+ E+R + +V+R G+ + S + +MVG Sbjct: 185 LFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMVG 244 Query: 259 RALDGEQRIPPDTSRNDVVLEVRGLN------RGRAIRDVSFTLRKGEILGFAGLMGAGR 312 A + P D L V GL+ G +++++ F +R GEI+G AG+ G G+ Sbjct: 245 EAAELITDY-PKVMGADAFLSVTGLSWHNPDPFGCSLKNIDFDVRSGEIVGVAGVAGNGQ 303 Query: 313 TEVARAIFGAD--PLEAGEIIIHGGKAVIKSPADAVAH-GIGYLSEDRKHFGLAVGMDVQ 369 E+ + G + P + I GG+ V DA G+ ++ +R G + + Sbjct: 304 DELLALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLA 363 Query: 370 ANIALSSMGR-FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428 N L++ + G + + ++ A+ +R+ +KTP AR LSGGN QK ++ + Sbjct: 364 DNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGR 423 Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488 +L+ +L PT G+DVGA + I++ L AL + G AI++IS +L E+ ++ R+ + Sbjct: 424 EILQQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRLGAL 483 Query: 489 CEGRITGELARAD 501 C G+++ A D Sbjct: 484 CGGQLSPLQATVD 496 Score = 98.6 bits (244), Expect = 5e-25 Identities = 67/219 (30%), Positives = 109/219 (49%), Gaps = 9/219 (4%) Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351 + ++ GEI G GAG++ + + I+G ++GE+I G + +++PA A GIG Sbjct: 32 IDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQGQRVTMRNPAQARGLGIG 91 Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQ 411 + + HF L + V NIAL+ MG + IRE +Q Y L E+ Sbjct: 92 MVFQ---HFSLFETLSVAQNIALA-MGAAAGTPKQLEPKIREVSQRYGMAL-----EPER 142 Query: 412 QARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMI 471 LS G +Q++ I + L++D +L DEPT + E++ L LA +G +I+ I Sbjct: 143 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLAAEGCSILFI 202 Query: 472 SSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQL 510 S +L EV + H V+ GR+ G A + ++ QL Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQL 241 Score = 63.2 bits (152), Expect = 2e-14 Identities = 56/232 (24%), Positives = 101/232 (43%), Gaps = 10/232 (4%) Query: 37 ALDNCQFELAAGEVHALMGENGAGKSTLMKILSG---VYQRDSGDILLDGKPVEITEPRQ 93 +L N F++ +GE+ + G G G+ L+ +LSG + + DS I G+PV P Sbjct: 279 SLKNIDFDVRSGEIVGVAGVAGNGQDELLALLSGEERLPRDDSATISFGGQPVAHLRPDA 338 Query: 94 AQALGIGIIHQEL---NLMNHLSAAQNIFIG--REPRKAMGLFIDEDELNRQAAAIFARM 148 + LG+ + E + LS A N + ++ + GL + ++ A I R Sbjct: 339 RRKLGLAFVPAERLGHGAVPELSLADNALLTAFQQGLVSHGL-VQRGKVQALAEDIIRRF 397 Query: 149 RLDM-DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQ 207 + D P L+ Q + + + ++L+ PT ++ A + R + L+ Sbjct: 398 GVKTPDSLAPARSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIALR 457 Query: 208 AQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGR 259 G I+ IS +DEL QI DR+ + G+ +T + + M G+ Sbjct: 458 DAGAAILVISEDLDELFQICDRLGALCGGQLSPLQATVDTHLSDVGGWMAGQ 509 Lambda K H 0.320 0.135 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: 611 Number of extensions: 48 Number of successful extensions: 9 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: 520 Length of database: 521 Length adjustment: 35 Effective length of query: 485 Effective length of database: 486 Effective search space: 235710 Effective search space used: 235710 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