Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SM_b20673 SM_b20673 sugar uptake ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Smeli:SM_b20673 Length = 526 Score = 439 bits (1128), Expect = e-127 Identities = 241/521 (46%), Positives = 341/521 (65%), Gaps = 17/521 (3%) Query: 3 LNTEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVY 62 + TE +R +L A I+K+F GV A+ +V ++ GE+ AL+GENGAGKSTLMK+L+GVY Sbjct: 10 VTTESDRPILA-AEAISKSFGGVAALKDVRFELRAGEIHALMGENGAGKSTLMKVLSGVY 68 Query: 63 PDYEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIE 122 DYEG + ++G+ VRF N R+A+ GIA+I QEL+LVP L A+NIFL RE V ++ Sbjct: 69 TDYEGAVRVDGETVRFSNVRDAEAAGIAIIHQELNLVPELGVADNIFLGRERVIAGLFVD 128 Query: 123 YQKMFEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGK 182 + E A L ++LG+ +DP+ +V L +QQ+V IAKALS++A+I+IMDEPTSA+ Sbjct: 129 RKASLEAARGLLNRLGIELDPEARVGQLRVGEQQLVEIAKALSVEARILIMDEPTSALSP 188 Query: 183 RETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLV 242 E +LF I+R L +G +IYISHR++E+ +++DRV V RDGR V P+ D + ++ Sbjct: 189 GECRRLFKIMRQLAADGVGIIYISHRIDEVMQLSDRVTVFRDGRHVWARPMAGLDENTII 248 Query: 243 RLMVGRSIDQFFIKERA--------TITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGE 294 MVGR++ ++R ++ D V G W + ++ VSF VR GE Sbjct: 249 AAMVGRNLLDAHRRDRGKGGGEPVLSVRDLSLAVSGRHGW-----RDVLKGVSFDVRAGE 303 Query: 295 VLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKT 354 +LGI GL+GAGRTE+LE IF ++ G G++ + G + I SPRDA + G LV EDRK Sbjct: 304 ILGIGGLLGAGRTEILETIFASNEGLRGGEIRLDGIAVNIRSPRDARRLGFALVTEDRKA 363 Query: 355 AGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENL 414 GL L S+ N+ LP V + +FGL + E+ + + ++ L ++ Q L Sbjct: 364 KGLHLHESIRDNVALPLVGR---LARFGLRSFEGERALAKGAVDALGVRCAGTGQAAGTL 420 Query: 415 SGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELP 474 SGGNQQKVV+ KWLA P+VLLLDEPTRGIDV AK EIY LI ++A G+ +V+VSSELP Sbjct: 421 SGGNQQKVVIGKWLATGPRVLLLDEPTRGIDVGAKREIYDLIFKLAGDGLAIVVVSSELP 480 Query: 475 EILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVK 515 E+L ++DRILVM+EGR+T REE +EE +++ A PRS + Sbjct: 481 ELLLLADRILVMAEGRQTGLISREEASEERIMQLAAPRSAR 521 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: 647 Number of extensions: 28 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 523 Length of database: 526 Length adjustment: 35 Effective length of query: 488 Effective length of database: 491 Effective search space: 239608 Effective search space used: 239608 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