Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 388 bits (996), Expect = e-112 Identities = 220/503 (43%), Positives = 321/503 (63%), Gaps = 20/503 (3%) Query: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDI 79 ++ +RN+ K FPGV+AL+ ++ AGE+HA++GENGAGKSTLMK+LSGVY S G I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139 L DG+ E R ++ LGI IIHQEL L+ LS A+NIF+G E A ID + Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNET--ARHGVIDWMAAHS 119 Query: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 +A A+ ++ L P TPVG+L V +QQ+VEIAKALS R+LI+DEPTA+LN + L Sbjct: 120 RAQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQAL 179 Query: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQE--TSMDTIISMMV 257 ++ +L+AQG+ + ISHK++E+ ++AD ++V+RDG + + +E S D +I MV Sbjct: 180 LDLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMV 239 Query: 258 GRALDGE--QRIPPDTSRNDVVLEVRGLNRGRA-------IRDVSFTLRKGEILGFAGLM 308 GR + QR P ++V EVR ++ + +R+GEI+G AGLM Sbjct: 240 GREMSDRYPQRQP---QVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLM 296 Query: 309 GAGRTEVARAIFGADPLE--AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGM 366 GAGRTE+A +IFG + +GE+ +HG + + AV+HG+ Y++EDRK GL + Sbjct: 297 GAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNE 356 Query: 367 DVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVI 426 D+Q N +L+++ + +D AQ Y +L I+ V+Q+ LSGGNQQK+V+ Sbjct: 357 DIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVL 416 Query: 427 AKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVL 486 +KWL ++L DEPTRGIDVGAK EIY L+ LA +GK +++ISSE+PE+L ++ R+ Sbjct: 417 SKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIY 476 Query: 487 VMCEGRITGELARADATQEKIMQ 509 VM EGR E+ ++A+QEKIM+ Sbjct: 477 VMNEGRFVAEMPTSEASQEKIMR 499 Score = 89.0 bits (219), Expect = 4e-22 Identities = 63/228 (27%), Positives = 114/228 (50%), Gaps = 10/228 (4%) Query: 38 LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY--QRDSGDILLDGKPVEITEPRQAQ 95 L + GE+ + G GAG++ L + G QR SG++ L G+P++++ +A Sbjct: 277 LKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAV 336 Query: 96 ALGIGIIHQELN---LMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRL-- 150 + G+ + ++ L+ + N + P + ID + +R A ++R+ Sbjct: 337 SHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRC 396 Query: 151 -DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQ 209 +D T L+ QQ V ++K L VLI+DEPT ++ E++ +I L A+ Sbjct: 397 SGVDQKTL--NLSGGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAE 454 Query: 210 GVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 G ++ IS +M EL I DR+ VM +G+++A +P E S + I+ +V Sbjct: 455 GKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIV 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: 654 Number of extensions: 32 Number of successful extensions: 9 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: 505 Length adjustment: 35 Effective length of query: 485 Effective length of database: 470 Effective search space: 227950 Effective search space used: 227950 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 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