Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Phaeo:GFF2274 Length = 503 Score = 361 bits (926), Expect = e-104 Identities = 204/501 (40%), Positives = 305/501 (60%), Gaps = 14/501 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +L + I KTFPGV+AL+ V+L + GE+HAL+GENGAGKSTLMKVL G++ EG+I Sbjct: 7 VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPD--EGQI 64 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 D++ GI+ IHQEL+L LS+AENI+LG G++ W + + Sbjct: 65 IVAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAK 124 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 T +L+K+ + + +T + D+ + QQ+VEIA+AL+ K +I DEPTASL +++ L Sbjct: 125 TNAILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLF 184 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 ++ + + QG+ I+H++ E+ K+ D+I+VLRDG T++ E +E+ + + M+G Sbjct: 185 EVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNT--AETNEENVTQMMIG 242 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R L+ +GE LEV+ + + D+N VR+GEVVG GL+GAGR Sbjct: 243 RKLDLSRNEAHHELGEVALEVRGLSC-------GSLFEDVNFEVRRGEVVGFYGLVGAGR 295 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 TE A ++FG + +G + +DG V +++ AI+ G++ V EDRK GLVL N Sbjct: 296 TEIAETLFGLR--NPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRD 353 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N TL + + + D E+ + +R +L IR+ G Q NLSGGNQQK+V+ KWL Sbjct: 354 NMTLPQVDDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWL 413 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 P+VLI+DEPTRGIDVG+K EI+ ++ LAA G V++ISSEMPE+L DRI M Sbjct: 414 SMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYS 473 Query: 484 GRIVAELPKGEASQESIMRAI 504 GRI+ E ++E+++ AI Sbjct: 474 GRIMRTFTSEEVTEENLIAAI 494 Score = 65.5 bits (158), Expect = 4e-15 Identities = 56/238 (23%), Positives = 111/238 (46%), Gaps = 27/238 (11%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L +++T+ GEV + G GAG++ M V G + G +++ +PV +S Sbjct: 21 RALDGVSLTILPGEVHALMGENGAGKSTL-MKVLGGIH-QPDEGQIIVAEQPVVMSGPLD 78 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIID----------DIKEMKV 387 A G+ ++ ++ L L ++ N L L + ++D ++++KV Sbjct: 79 AKAKGIVFIHQE---LSLADELSVAENIYLGELPR-KRFGLVDWAELEAKTNAILEKLKV 134 Query: 388 ASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEI 447 + +TR+ +LS NQQ V +++ L + +I DEPT + K + Sbjct: 135 GFNAKTRVG-----------DLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVL 183 Query: 448 YTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505 + +I+ L G G+ IS M E+ DRI V+ +G+ + E ++E++ + ++ Sbjct: 184 FEVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMI 241 Lambda K H 0.316 0.135 0.374 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: 648 Number of extensions: 38 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: 512 Length of database: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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