Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 443 bits (1139), Expect = e-129 Identities = 245/507 (48%), Positives = 342/507 (67%), Gaps = 10/507 (1%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +LEM+NITKTF VKA++NV L++ GEI +L GENG+GKSTLMKVL G+YP G+YEGEI Sbjct: 4 LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124 + G I D+E GI IIHQELALV L++ ENIFLGNE+ NG++ + R Sbjct: 64 IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123 Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184 ++LL +V L SP+T + D+G+G+QQLVEIAKAL+K V+LLILDEPTASL E ++ LL+ Sbjct: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183 Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244 ++ + + G+ I I+HKLNEV+ ++D I V+RDG + T D +SED II MVGR Sbjct: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDA--AGMSEDDIITMMVGR 241 Query: 245 DLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRT 304 +L YP G+ IL +++ A+H +R + ++D++ ++++GE++GIAGL+GAGRT Sbjct: 242 ELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRT 301 Query: 305 EFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHN 364 E +FG G + G + IDGK VD+ ++AI G+A V EDRK G+V + N Sbjct: 302 ETIQCLFGVWPG-QWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKN 360 Query: 365 TTLANL----AGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 TLA L G+S+ +DD E K + +L++++S LSGGNQQK +L+ Sbjct: 361 ITLAALNKFTGGISQ---LDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILA 417 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 + L NP +LILDEPTRGID+GAKYEIY +INQL G V++ISSE+PE+LG DR+ V Sbjct: 418 RCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLV 477 Query: 481 MNEGRIVAELPKGEASQESIMRAIMRS 507 M+EG++ A L +QE +M A +RS Sbjct: 478 MHEGKLKANLINHNLTQEQVMEAALRS 504 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: 682 Number of extensions: 38 Number of successful extensions: 8 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: 513 Length adjustment: 35 Effective length of query: 477 Effective length of database: 478 Effective search space: 228006 Effective search space used: 228006 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