Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 327 bits (839), Expect = 5e-94 Identities = 191/503 (37%), Positives = 293/503 (58%), Gaps = 11/503 (2%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81 VI ++++ K FPG++A DN ++ GE+HAL+GENGAGKSTLM +L G+YQ + G+IL+ Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 82 DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141 GKPV+IT+P A LGIG++HQ L+ + +NI +G+EP G I+ + + Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEP--TAGGKINIKKAAKAV 121 Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201 I + L +DP + +++V QQ VEI K L + +LI DEPTAAL EI EL + Sbjct: 122 ETISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQ 181 Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261 I++ L ++G I+ I+HK+ E+ ++ DR +V+R G+ I TV + E++ D++ +MMVGR + Sbjct: 182 IMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREV 241 Query: 262 DGEQRIPPDTSRNDVVLEVRGL-----NRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316 + P D VL+++ L A+ D+ + GEILG AG+ G G+TE+ Sbjct: 242 NFSVEKDP-AQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELI 300 Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376 AI G G I ++G +P G+G++ +DR GL + V NI L + Sbjct: 301 EAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQT 360 Query: 377 MGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDC 434 + ++ G ++ I + A + ++TPS AR LSGGNQQK +IA+ + R Sbjct: 361 YYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSP 420 Query: 435 DILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRIT 494 D+L +PTRG+DVGA I+ L ++GKA+++IS EL EVL +S R+ V+ EG+I Sbjct: 421 DLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIV 480 Query: 495 GELARADATQEKIMQLATQRESA 517 + AD T E + L SA Sbjct: 481 A-IVDADKTNENELGLLMAGGSA 502 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: 607 Number of extensions: 35 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: 520 Length of database: 509 Length adjustment: 35 Effective length of query: 485 Effective length of database: 474 Effective search space: 229890 Effective search space used: 229890 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 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