Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_002117405.1:WP_085770502.1 Length = 293 Score = 114 bits (285), Expect = 5e-30 Identities = 84/278 (30%), Positives = 135/278 (48%), Gaps = 20/278 (7%) Query: 4 DKETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKST 63 D++ + ++ + +AL N+ F G+ AL F +AAGE+ +++G NGAGKS+ Sbjct: 16 DEDAQSWSLSDDHARGGATLALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSS 75 Query: 64 LMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGRE 123 L+ +++G+Y+ D G I LD + +LG+ Q L L LS NI +GR Sbjct: 76 LINVITGLYRPDWGRIQLDKNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRV 135 Query: 124 P-------RKAMGLFIDEDELNRQAAAIFAR-----MRLDMDPSTPVGELTVARQQMVEI 171 + GL +R A I + L + G L Q+ VE+ Sbjct: 136 SATRSHWLEQVFGL--PRARADRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVEL 193 Query: 172 AKALSFDSRVLIMDEPTAAL---NNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIAD 228 A+AL+ R+L++DEP A + AE+ E ++ RD G IV I H + + +++D Sbjct: 194 ARALAIRPRLLLLDEPMAGMTAGEKAEMGEFIQLTRD--RFGASIVLIEHDIGVVMELSD 251 Query: 229 RVSVMRDGKYIATVPMQETSMD-TIISMMVGRALDGEQ 265 RV+V+ G+ IA P + D +I +G A D EQ Sbjct: 252 RVAVLDYGRKIADGPPSDVMNDEAVIDAYLGVAHDIEQ 289 Score = 59.7 bits (143), Expect = 1e-13 Identities = 55/217 (25%), Positives = 109/217 (50%), Gaps = 15/217 (6%) Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346 +A+ ++ F++ GEI G GAG++ + I G + G I + + + P + + Sbjct: 48 QALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLDKN-SFSRMPTERL 106 Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQ-------RAIREAAQMYV 399 A +G ++ ++ L G+ V NIA+ + TR +++Q RA R A ++ V Sbjct: 107 A-SLG-VARTFQNLALFRGLSVFDNIAVGRVSA-TRSHWLEQVFGLPRARADRLATEIIV 163 Query: 400 RQLAIKTPSVEQQARL---LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYK 456 ++ + + + R+ L G Q+++ +A+ L +L DEP G+ G K+E+ + Sbjct: 164 EEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMTAGEKAEMGE 223 Query: 457 LLDALAEQ-GKAIVMISSELPEVLRMSHRVLVMCEGR 492 + ++ G +IV+I ++ V+ +S RV V+ GR Sbjct: 224 FIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGR 260 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: 317 Number of extensions: 16 Number of successful extensions: 5 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: 293 Length adjustment: 30 Effective length of query: 490 Effective length of database: 263 Effective search space: 128870 Effective search space used: 128870 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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