Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 256 bits (653), Expect = 2e-72 Identities = 166/509 (32%), Positives = 277/509 (54%), Gaps = 21/509 (4%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M +E++ I+K F V+A ++++++V G IH ++GENGAGKSTLM +L G Y A Sbjct: 1 MTAPAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKAD-- 58 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 +GE+ G + GI ++ Q LV ++ ENI LG E S + Sbjct: 59 KGEVWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKA 118 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 ++L + L P+ I +IGVG QQ VEI KAL + +LILDEPT L ++++ Sbjct: 119 RKSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEAD 178 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDG---MTVKTLDCHQEEISEDVI 237 L +L R +G T I+ITHKL E+ + D ++V+R G TVKT + E ++E Sbjct: 179 QLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAE--- 235 Query: 238 IRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAG 297 MVGR + R G+ ILE++N + + R + +I++TVR GE++GIAG Sbjct: 236 --LMVGRKVLLRVDKVPATPGKPILEIENLSVVDEAGVAR--VKNIDLTVRAGEILGIAG 291 Query: 298 LMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVS----TVRKAIDAGLAYVTEDRKHL 353 + G G++E + G G G + ++G P+ +S R A +A+V EDR+ Sbjct: 292 VAGNGQSELMEVLGGMREGQ---GSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQRE 348 Query: 354 GLVLNDNILHNTTLA-NLAGVSKASIIDDIKEMKVASDFR-TRLRIRSSGIFQETVNLSG 411 GL+++ + N + A + ++ + ++ ++ + + +R + N SG Sbjct: 349 GLIMDFHAWENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSG 408 Query: 412 GNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPEL 471 GNQQK+V+++ + NP++L++ +PTRG+D+GA I+ I +L GK +L++S E+ E+ Sbjct: 409 GNQQKIVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEI 468 Query: 472 LGNCDRIYVMNEGRIVAELPKGEASQESI 500 L DR+ VM +G I+ E P + ++ + Sbjct: 469 LSLADRVAVMFDGMIMGERPADQTDEKEL 497 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: 616 Number of extensions: 29 Number of successful extensions: 10 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: 512 Length of database: 509 Length adjustment: 35 Effective length of query: 477 Effective length of database: 474 Effective search space: 226098 Effective search space used: 226098 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