Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 307 bits (787), Expect = 5e-88 Identities = 182/503 (36%), Positives = 302/503 (60%), Gaps = 13/503 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ILE++ I+K +PGVKALE+V+L++ GE+HAL+GENGAGKSTL+KV++G G+I Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDM--GDI 61 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 + G ++F D++ GI ++QE+ LVP L++A+N+FLG E G+I +++ + Sbjct: 62 LFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADA 121 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 R +L + L ++D + QQL+ IA+ ++ S K+L+LDEPTASL+ + + L Sbjct: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 +L + + +G+ + ITH L++V +++D+ITVLR+G + + E+ + +I M+GR Sbjct: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIG--EYLTAELPQPKLIEAMLGR 239 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQV---LHDINVTVRKGEVVGIAGLMGA 301 L+++ + E V A D V + +N+TV KG+ VG+AGL+G+ Sbjct: 240 SLQEQLVDKQ----EKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGS 295 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GR+E +VFG +G + + G+ +++S AI AG+A EDRK G++ +I Sbjct: 296 GRSEVCNAVFGLDLVD--SGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSI 353 Query: 362 LHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421 N LA A + + + ++ ++A F +L+I + + LSGGNQQKV+L++ Sbjct: 354 RENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILAR 413 Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481 WL P +L+LDEPTRGID+GA EI +I L +G +L+ SSE+ EL+ +++ V+ Sbjct: 414 WLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 Query: 482 NEGRIVAELPKGEASQESIMRAI 504 + V EL E + + +M+AI Sbjct: 474 RDRYAVRELSGAELTSQHVMQAI 496 Score = 68.9 bits (167), Expect = 4e-16 Identities = 60/245 (24%), Positives = 114/245 (46%), Gaps = 11/245 (4%) Query: 261 ILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRIT 320 ILE+K + ++ + L D+++ + GEV + G GAG++ + G + Sbjct: 4 ILELKQISKHYPGVK---ALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQ--SKDM 58 Query: 321 GDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIID 380 GD+L G+P +T A AG++ V ++ + LV N + N L + +I Sbjct: 59 GDILFLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEP--RRLGLIH 113 Query: 381 DIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGID 440 K A T+ ++ + + S QQ + +++ + + VL+LDEPT +D Sbjct: 114 FKKMYADARAVLTQFKL-DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLD 172 Query: 441 VGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESI 500 ++ I+NQL A G ++ I+ + ++ DRI V+ G+ + E E Q + Sbjct: 173 AKEVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKL 232 Query: 501 MRAIM 505 + A++ Sbjct: 233 IEAML 237 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: 549 Number of extensions: 31 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: 499 Length adjustment: 34 Effective length of query: 478 Effective length of database: 465 Effective search space: 222270 Effective search space used: 222270 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