Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 335 bits (860), Expect = 2e-96 Identities = 192/505 (38%), Positives = 298/505 (59%), Gaps = 15/505 (2%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 M +L +R +++ F V+ L +V+ ++ GE+HAL+GENGAGKST MK+L+G Sbjct: 1 MTEPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSA- 59 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 GE+ +G +F + ++E G+++IHQE L L++ ENIFLG E+ + + Sbjct: 60 -GEVLLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAM 118 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 +R LL+++ P ++ + V +Q+VEIAKAL ++LI+DEPTA L +++ Sbjct: 119 QAESRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETD 178 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 LL + R G + +HKL+EV ++AD++TVLRDG V T + +SED + Sbjct: 179 TLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPA--KGLSEDRMAET 236 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR+L +PP+ P E +LEV + D + T+R+GEV+G AGL+G Sbjct: 237 MVGRELSGLFPPKSSPAPEPVLEVAGLTV-------PGFVRDASFTLRRGEVLGFAGLVG 289 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 +GRTE + G TG+V ++G P+ ++V A AGL Y+TEDRK GL+L Sbjct: 290 SGRTELMEGIVGL---RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKP 346 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 + N TL L + +ID E + + + IR +LSGGNQQK++L+ Sbjct: 347 LGENLTLLALDRFGRV-LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLA 405 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 K + + P V+I+DEPTRGIDVG K +IY I +LAA+G+ V+++SSE+PE++G +R+ V Sbjct: 406 KTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVV 465 Query: 481 MNEGRIVAELPKGEASQESIMRAIM 505 M+ GRI E+ ++E+I+R M Sbjct: 466 MSAGRIAGEVEGEAITEENIVRLAM 490 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: 597 Number of extensions: 38 Number of successful extensions: 12 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: 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 24 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