Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_041936920.1 RL_RS31840 sugar ABC transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000009265.1:WP_041936920.1 Length = 511 Score = 367 bits (942), Expect = e-106 Identities = 199/503 (39%), Positives = 310/503 (61%), Gaps = 14/503 (2%) Query: 2 ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61 A ILEMR I++ FPGVKAL+NV++ + G + AL+GENGAGKSTL+K+L+G+Y E Sbjct: 17 APAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPN--E 74 Query: 62 GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQT 120 GEI +G F + + D G+ IHQE L L++AENIFLG+ + I WQ Sbjct: 75 GEILVDGQPVTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRLRTIDWQAM 134 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 +R + LL + P + D + ++ LV IA+ALS +++I+DEPTA+L+ + + Sbjct: 135 NSRAKALLTALESNIDPTIRLKDFSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEID 194 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L ++ + +G + I+HK +EV ++AD V RDG V +E +D I+R Sbjct: 195 DLFRIVRGLKEKGKAILFISHKFDEVYEIADDFVVFRDGRAVG--QGRLKETPQDEIVRM 252 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGRD+E+ +P DV G +LE++N++ R DI+ T+R+GE++GI GL+G Sbjct: 253 MVGRDVENAFPKVDVAFGGPVLEIRNYS-------HRTEFRDISFTLRQGEILGIYGLIG 305 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGR+E + S+FG + ++G ++++G+ + + + + AI AG+ YV E+R GL L Sbjct: 306 AGRSELSQSLFGIT--RPLSGKMMLEGREITIHSPQDAIRAGIVYVPEERGRHGLALPMP 363 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 I N TL +L S+ + +E +A + RL +R++ + LSGGNQQKVV+ Sbjct: 364 IFQNMTLPSLTRTSRRGFLRAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 423 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWL + P V+ILDEPT+GID+G+K ++ I++LAA+G ++M+SSE+PE++G DR+ V Sbjct: 424 KWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLV 483 Query: 481 MNEGRIVAELPKGEASQESIMRA 503 M EG + E S E+++RA Sbjct: 484 MKEGLAAGIFERAELSPEALVRA 506 Score = 67.8 bits (164), Expect = 9e-16 Identities = 55/239 (23%), Positives = 111/239 (46%), Gaps = 15/239 (6%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L ++++ + G V + G GAG++ + G + G++L+DG+PV ++ + Sbjct: 34 KALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNE--GEILVDGQPVTFASAQA 91 Query: 338 AIDAGLAYVTEDRKHLG-LVLNDNI-LHNTTLANLAGVSKASIIDDIKEMKVA--SDFRT 393 AIDAG+ + ++ L + +NI L + L + ++ K + A S+ Sbjct: 92 AIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRLRTIDWQAMNSRAKALLTALESNIDP 151 Query: 394 RLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQ 453 +R++ I Q + V +++ L ++I+DEPT + +++ I+ Sbjct: 152 TIRLKDFSIAQRHL---------VAIARALSIEARIVIMDEPTAALSRKEIDDLFRIVRG 202 Query: 454 LAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGEKNS 512 L GK +L IS + E+ D V +GR V + E Q+ I+R ++ +N+ Sbjct: 203 LKEKGKAILFISHKFDEVYEIADDFVVFRDGRAVGQGRLKETPQDEIVRMMVGRDVENA 261 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: 629 Number of extensions: 32 Number of successful extensions: 10 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: 511 Length adjustment: 35 Effective length of query: 477 Effective length of database: 476 Effective search space: 227052 Effective search space used: 227052 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