Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >NCBI__GCF_000342445.1:WP_008497300.1 Length = 310 Score = 113 bits (283), Expect = 9e-30 Identities = 72/226 (31%), Positives = 126/226 (55%), Gaps = 9/226 (3%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFL 71 +L+ +TK F +AV+ VT+++ +GE L+G NGAGKST + +++ + G + L Sbjct: 1 MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60 Query: 72 EGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENI-FLSREPVNEFGVIEYQKMFEQA 130 GK V + P E ++ + ++PQ++ L LS+ EN+ F R +G + +K+ E+ Sbjct: 61 NGKSV-LKKPGEMRK-VLGVVPQKIALYEELSAYENLKFFGR----IYG-LSGKKLEERI 113 Query: 131 SKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFN 190 + +G++ K V+ S Q+ V +A A+ + +++IMDEPT I + L Sbjct: 114 QIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGIDPQSRNHLLE 173 Query: 191 IIRSLKNE-GKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEE 235 IR L E G +V+Y SH +EE+ ++ DRV +M G+ + G +E Sbjct: 174 TIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDE 219 Score = 80.9 bits (198), Expect = 6e-20 Identities = 64/230 (27%), Positives = 119/230 (51%), Gaps = 16/230 (6%) Query: 272 KLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKE 331 KL + L VD+V+ + +GE +G+ G GAG++ + I T G V + GK Sbjct: 6 KLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMI-STLIQPTSGDVRLNGKS 64 Query: 332 IKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKE 391 + + P + ++ +G+VP+ L ++S N+ K R +GL +LE+ Sbjct: 65 V-LKKPGE-MRKVLGVVPQK---IALYEELSAYENL-------KFFGRIYGLSGKKLEER 112 Query: 392 IVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSE 451 I + +L + ++V+ SGG Q++V LA + +P+VL++DEPT GID +++ Sbjct: 113 I--QIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGIDPQSRNH 170 Query: 452 IYKLISEM-AVSGMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEV 500 + + I ++ GM V+ S + E+ + DR+ +M G+ A ++E+ Sbjct: 171 LLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDEL 220 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: 382 Number of extensions: 21 Number of successful extensions: 6 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: 310 Length adjustment: 31 Effective length of query: 492 Effective length of database: 279 Effective search space: 137268 Effective search space used: 137268 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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