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:D8IZC7 (521 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 369 bits (946), Expect = e-106 Identities = 212/501 (42%), Positives = 316/501 (63%), Gaps = 14/501 (2%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV--HAPDQGEI 63 LL+MR IRK+F +AL+ ++L ++ GEIHA++GENGAGKSTLMKVLSGV H G+I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123 L DG+ S GI +I+QELA+ P +S+A N+F+G+E R G+ID A SR Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNET-ARHGVIDWMAAHSR 120 Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183 A+L ++G G G+L + +QQ VEIA+AL + R++I+DEPTA+L+E +++ L Sbjct: 121 AQALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180 Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDE--IDSERIVQMMVG 241 +++ L+ +G+ I ISH++ E+ +AD +TVLRDGS V L E + +R++Q MVG Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVG 240 Query: 242 RSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK-----IRPASFDVRAGEVLGFAGLVGA 296 R +S+ Y ++ P + V RA + ++ +VR GE++G AGL+GA Sbjct: 241 REMSDRYPQRQ--PQVGEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGA 298 Query: 297 GRTELARLLFGAD--PRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAV 354 GRTELA +FG R G++ L G+P+ + A+ G+AYV EDRKG GL L + Sbjct: 299 GRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLVLNEDI 358 Query: 355 AANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLAR 414 N ++ + ++ S VA+ ++L ++ + + LSGGNQQKV+L++ Sbjct: 359 QFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQKVVLSK 418 Query: 415 WLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVM 474 WL +P+VLILDEPTRG+D+ AK EIY L+ +LA++G V+VISSE+PE++GI DR+ VM Sbjct: 419 WLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITDRIYVM 478 Query: 475 REGMITGELAGAAITQENIMR 495 EG E+ + +QE IMR Sbjct: 479 NEGRFVAEMPTSEASQEKIMR 499 Score = 76.6 bits (187), Expect = 2e-18 Identities = 61/241 (25%), Positives = 109/241 (45%), Gaps = 31/241 (12%) Query: 22 LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ--GEILLDGRPVALRDPGASR 79 L + L +R GEI + G GAG++ L + G + GE+ L G+P+ + + Sbjct: 277 LKGIDLNVRRGEIVGIAGLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAV 336 Query: 80 AAGINLIYQE-----------------LAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 122 + G+ + ++ LA P +S A+ + G E R A Sbjct: 337 SHGLAYVTEDRKGNGLVLNEDIQFNTSLANLPGVSFASVIDSGQEHRV--------AQDY 388 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 R +R G +L+G QQ+V +++ L ++I+DEPT + ++ Sbjct: 389 REKLRIRCSGVDQKTLNLSG----GNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEI 444 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 + ++ +L EG +I IS M E+ + DR+ V+ +G FV E+ E E+I++ +V Sbjct: 445 YTLIAQLAAEGKCVIVISSEMPELLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIVKA 504 Query: 243 S 243 S Sbjct: 505 S 505 Lambda K H 0.320 0.135 0.378 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: 677 Number of extensions: 32 Number of successful extensions: 11 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: 521 Length of database: 505 Length adjustment: 35 Effective length of query: 486 Effective length of database: 470 Effective search space: 228420 Effective search space used: 228420 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