Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_011428142.1 RHE_RS25530 ribose import ATP-binding protein RbsA 3
Query= TCDB::O05176 (512 letters) >NCBI__GCF_000092045.1:WP_011428142.1 Length = 511 Score = 371 bits (952), Expect = e-107 Identities = 202/503 (40%), Positives = 316/503 (62%), 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 GEILVDGQPTSFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRLRTIDWQTM 134 Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180 +R++ LL + P + D+ + ++ LV IA+ALS +++I+DEPTA+L+ + + Sbjct: 135 NSRSKTLLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEID 194 Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240 L ++ ++QG + I+HK +E+ ++AD V RDG V +E +D I+R Sbjct: 195 DLFRIVRGLKDQGKAILFISHKFDELYEIADDFVVFRDGRAVG--QGRLKETPQDEIVRM 252 Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 MVGRD+E+ +P DV IG +LEV +++ R D+++T+R+GE++GI GL+G Sbjct: 253 MVGRDVENVFPKIDVAIGGPVLEV-------EKYCHRTEFRDVSLTLRRGEILGIYGLIG 305 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGR+E A S+FG + ++G + ++G+ + +++ AI AG+ YV E+R GL L Sbjct: 306 AGRSELAQSLFGVT--KPLSGRLTLEGREISINSPHDAIKAGIVYVPEERGRHGLALPMP 363 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 I N TL +LA S+ + +E +A + RL +R++ + LSGGNQQKVV+ Sbjct: 364 IYQNMTLPSLARTSRKGFLKAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIG 423 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWL + P V+ILDEPT+GID+G+K ++ I++LAA+G ++MISSE+PE++G DR+ V Sbjct: 424 KWLATMPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMISSELPEIIGMSDRVLV 483 Query: 481 MNEGRIVAELPKGEASQESIMRA 503 M EG V + + S E+++RA Sbjct: 484 MKEGLSVGLFERDQLSPEALVRA 506 Score = 69.7 bits (169), Expect = 2e-16 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 15/238 (6%) Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337 + L ++++ + G V + G GAG++ + G + G++L+DG+P ++ + Sbjct: 34 KALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNE--GEILVDGQPTSFASAQA 91 Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANL-AGVSKASIIDDIKEMKVASDFRTRLR 396 AIDAG+ + H VL D + T N+ G + + + I + S +T L Sbjct: 92 AIDAGVTAI-----HQETVLFDEL---TVAENIFLGHAPRTRLRTIDWQTMNSRSKTLLT 143 Query: 397 IRSSGIFQETV---NLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQ 453 S I T+ +LS + V +++ L ++I+DEPT + +++ I+ Sbjct: 144 ALESNI-DPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRIVRG 202 Query: 454 LAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511 L GK +L IS + EL D V +GR V + E Q+ I+R ++ +N Sbjct: 203 LKDQGKAILFISHKFDELYEIADDFVVFRDGRAVGQGRLKETPQDEIVRMMVGRDVEN 260 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: 621 Number of extensions: 25 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