Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_040659172.1 ON16_RS02720 ATP-binding cassette domain-containing protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000307265.1:WP_040659172.1 Length = 516 Score = 612 bits (1579), Expect = e-180 Identities = 308/507 (60%), Positives = 400/507 (78%) Query: 1 MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60 MA+ +LEMR+I K FPGV+AL+NVNL+V++GEIHALVGENGAGKSTLM VLSG+YP GTY Sbjct: 1 MASKLLEMRSIIKEFPGVRALDNVNLEVEQGEIHALVGENGAGKSTLMNVLSGIYPYGTY 60 Query: 61 EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120 +G+I Y+G V F INDSE G++IIHQELALVP L+I EN+FLGNE I W +T Sbjct: 61 QGDIVYDGEVCKFGKINDSESKGVVIIHQELALVPYLTIGENMFLGNEQGRASRIDWDKT 120 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 ++ + LK VGL+ESP TLI DIGVGKQQLVEIAKAL+K+V+LLILDEPTASLNE+DS+ Sbjct: 121 YDLAAKYLKTVGLEESPRTLIKDIGVGKQQLVEIAKALTKNVRLLILDEPTASLNETDSQ 180 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 LL+LL++F+ QGMT III+HKL+EV VAD+IT++RDG T++TL ++ E+ II+ Sbjct: 181 KLLDLLLQFKAQGMTCIIISHKLSEVSYVADKITIIRDGATIETLVKGVDDFHEERIIKG 240 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGR+L DR+P R+ IG+ ++EV++W A H + R V + +++ VR+GE+VG++GLMG Sbjct: 241 MVGRELVDRFPKRESHIGDVVMEVQDWCAEHPTYAGRMVCNHVSMNVRRGEIVGVSGLMG 300 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGRTE AMS+FG+SYG I G +L++G+ V + +V AI+ LAYVTEDRK GL+L++ Sbjct: 301 AGRTELAMSIFGRSYGANIKGSLLLNGQEVRLHSVTDAINHKLAYVTEDRKGNGLILSET 360 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 I NTT+A + +S+ ++D E+K A++++ LR + +GI Q NLSGGNQQKV+LS Sbjct: 361 IRENTTMARMERISRHQVLDKDLEIKYANEYKEILRTKCAGIEQNVGNLSGGNQQKVLLS 420 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KW+F+ PDVLILDEPTRGIDVGAKYEIY I+N L + GK VLMISSEMPELLG CDRIYV Sbjct: 421 KWMFAEPDVLILDEPTRGIDVGAKYEIYCIMNDLVSQGKAVLMISSEMPELLGMCDRIYV 480 Query: 481 MNEGRIVAELPKGEASQESIMRAIMRS 507 MNEG +V EL +ASQESIM I++S Sbjct: 481 MNEGSVVGELTHEQASQESIMACILKS 507 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: 762 Number of extensions: 22 Number of successful extensions: 5 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: 516 Length adjustment: 35 Effective length of query: 477 Effective length of database: 481 Effective search space: 229437 Effective search space used: 229437 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