Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 437 bits (1125), Expect = e-127 Identities = 247/513 (48%), Positives = 328/513 (63%), Gaps = 10/513 (1%) Query: 13 AASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72 + ++ S P++A + K F GV AL + +FEL AGE+HALMGENGAGKSTLMK+LSGVY Sbjct: 9 SVTTESDRPILAAEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVY 68 Query: 73 QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132 G + +DG+ V + R A+A GI IIHQELNL+ L A NIF+GRE R GLF+ Sbjct: 69 TDYEGAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRE-RVIAGLFV 127 Query: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192 D A + R+ +++DP VG+L V QQ+VEIAKALS ++R+LIMDEPT+AL+ Sbjct: 128 DRKASLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALS 187 Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252 E LF+I+R L A GVGI+YISH++DE+ Q++DRV+V RDG+++ PM +TI Sbjct: 188 PGECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTI 247 Query: 253 ISMMVGRALDGEQRIPPDTSRNDVVLEVRGLN---RGR-----AIRDVSFTLRKGEILGF 304 I+ MVGR L R + VL VR L+ GR ++ VSF +R GEILG Sbjct: 248 IAAMVGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGI 307 Query: 305 AGLMGAGRTEVARAIFGADP-LEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLA 363 GL+GAGRTE+ IF ++ L GEI + G I+SP DA G ++EDRK GL Sbjct: 308 GGLLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLH 367 Query: 364 VGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQK 423 + ++ N+AL +GR R G R A+ V L ++ Q A LSGGNQQK Sbjct: 368 LHESIRDNVALPLVGRLARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTLSGGNQQK 427 Query: 424 IVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSH 483 +VI KWL +L DEPTRGIDVGAK EIY L+ LA G AIV++SSELPE+L ++ Sbjct: 428 VVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLAD 487 Query: 484 RVLVMCEGRITGELARADATQEKIMQLATQRES 516 R+LVM EGR TG ++R +A++E+IMQLA R + Sbjct: 488 RILVMAEGRQTGLISREEASEERIMQLAAPRSA 520 Score = 92.8 bits (229), Expect = 3e-23 Identities = 74/255 (29%), Positives = 123/255 (48%), Gaps = 15/255 (5%) Query: 21 PVIALRNVCKRFPGVLA----LDNCQFELAAGEVHALMGENGAGKSTLMK-ILSGVYQRD 75 PV+++R++ G L F++ AGE+ + G GAG++ +++ I + Sbjct: 271 PVLSVRDLSLAVSGRHGWRDVLKGVSFDVRAGEILGIGGLLGAGRTEILETIFASNEGLR 330 Query: 76 SGDILLDGKPVEITEPRQAQALGIGIIHQELN---LMNHLSAAQNI---FIGREPRKAMG 129 G+I LDG V I PR A+ LG ++ ++ L H S N+ +GR R + Sbjct: 331 GGEIRLDGIAVNIRSPRDARRLGFALVTEDRKAKGLHLHESIRDNVALPLVGRLARFGLR 390 Query: 130 LFIDEDELNRQAA-AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPT 188 F E L + A A+ R G L+ QQ V I K L+ RVL++DEPT Sbjct: 391 SFEGERALAKGAVDALGVRCA---GTGQAAGTLSGGNQQKVVIGKWLATGPRVLLLDEPT 447 Query: 189 AALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETS 248 ++ E++ +I L G+ IV +S ++ EL +ADR+ VM +G+ + +E S Sbjct: 448 RGIDVGAKREIYDLIFKLAGDGLAIVVVSSELPELLLLADRILVMAEGRQTGLISREEAS 507 Query: 249 MDTIISMMVGRALDG 263 + I+ + R+ G Sbjct: 508 EERIMQLAAPRSARG 522 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: 720 Number of extensions: 40 Number of successful extensions: 10 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: 520 Length of database: 526 Length adjustment: 35 Effective length of query: 485 Effective length of database: 491 Effective search space: 238135 Effective search space used: 238135 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