Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_052665037.1 NITAL_RS04930 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_000969705.1:WP_052665037.1 Length = 511 Score = 420 bits (1079), Expect = e-122 Identities = 231/510 (45%), Positives = 338/510 (66%), Gaps = 14/510 (2%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDI 79 ++ +R + K FPGV AL++ +A GE+HA+ GENGAGKSTLM +LSGVY + G+I Sbjct: 4 ILEMREITKTFPGVKALEDVNLTVARGEIHAICGENGAGKSTLMNVLSGVYPAGTYTGEI 63 Query: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139 + DG+PVE ++ALGI IIHQEL L+ HLS A+NIF+G E + ID E NR Sbjct: 64 VFDGEPVEHQSINDSEALGIVIIHQELALIPHLSVAENIFLGNEQSRRG--VIDWHETNR 121 Query: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 A + R+ LD +P+TPVG+L V +QQ++EIAKALS D ++LI+DEPTAALN+ + A L Sbjct: 122 MAGELLQRVGLDENPTTPVGQLGVGKQQLIEIAKALSKDVKLLILDEPTAALNDQDSAHL 181 Query: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQE--TSMDTIISMMV 257 ++R L+A+G+ + ISHK++EL +IAD +++RDG+ I T+ M + ++ +I MV Sbjct: 182 LGLLRQLRAEGITCIMISHKLNELLEIADATTIIRDGRTIETLDMSDPDSNQRRMIRGMV 241 Query: 258 GRALDG-----EQRIPPDTSRNDVVLEVRGLNRGRAIRD-VSFTLRKGEILGFAGLMGAG 311 GR +D + + + R + + GR I + + ++R GEI+G AGLMGAG Sbjct: 242 GRDIDSLYPERQATLGEEVFRVEDWTVMHPTQAGRVIVEGANLSVRAGEIVGIAGLMGAG 301 Query: 312 RTEVARAIFGADPLE--AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQ 369 RTE+A +IFG +G++ +HG + + A++HGI Y +EDRK +GL + D++ Sbjct: 302 RTELAMSIFGRTYGRDVSGQVYMHGQQVDTHTVDAAISHGIAYATEDRKRYGLNLIEDIR 361 Query: 370 ANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKW 429 NI+ S++G+ + G++D A+ Y R L I+ PSV LSGGNQQK+V++KW Sbjct: 362 RNISASALGKLSHNGWVDGNQEIAVAERYRRDLDIRAPSVMSVVGKLSGGNQQKVVLSKW 421 Query: 430 LLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMC 489 L D ++L DEPTRGIDVGAK EIY +++ LAE GKA+++ISSELPE+L + R+ + Sbjct: 422 LYTDPELLILDEPTRGIDVGAKFEIYTIVNRLAEAGKAVLVISSELPELLGICDRIYTLS 481 Query: 490 EGRITGELARADATQEKIMQLATQRESAVA 519 GRITGEL A+ATQE++M+L T + V+ Sbjct: 482 AGRITGELPAAEATQERLMELMTMVKDEVS 511 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: 701 Number of extensions: 37 Number of successful extensions: 9 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: 511 Length adjustment: 35 Effective length of query: 485 Effective length of database: 476 Effective search space: 230860 Effective search space used: 230860 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 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