Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 303 bits (775), Expect = 1e-86 Identities = 175/475 (36%), Positives = 276/475 (58%), Gaps = 12/475 (2%) Query: 8 VVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVD 67 V + +T EF V+ L GV L PG V+ L+GENGAGKST++K L G G ++VD Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 68 GKPQQFNGTLDAQNA-GIATVYQEVNLCTNLSVGENVMLGHE-KRGPFGIDWKKTHEAAK 125 G + G A A GI ++QE NL +L++ +N+ LGHE KRG F +D K E + Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLF-LDDKAMREKTR 123 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 + LA++GL +DP T + + +A +QLV IARA+ NA++LI+DEPT++L E LFA Sbjct: 124 EALAKVGLP-LDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFA 182 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 +M ++ +GV I+++SH LD++ TD + ++R+G + T R ++ +M+G+ Sbjct: 183 LMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGREL 242 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTEL 305 A+L + P + V+GL G VD ++ +GE++GFAGL+G+GRTEL Sbjct: 243 ADLF-----PPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTEL 297 Query: 306 GRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIA 365 L G +GT + G+ V + P A ++ + Y +E+R+ +G+ +R N + Sbjct: 298 FEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPN--LT 355 Query: 366 LQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHP 424 L A KP + A + + ++E +R + +LSGGNQQK+ + + L P Sbjct: 356 LMALERYAKPWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGP 415 Query: 425 ELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLK 479 +++LDEPTRG+D+GAK EI +V LA QG+ V+ ISSEL E++ L + V++ Sbjct: 416 SVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMR 470 Score = 88.2 bits (217), Expect = 6e-22 Identities = 57/244 (23%), Positives = 121/244 (49%), Gaps = 8/244 (3%) Query: 3 DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62 D P + ++G+T+ PG +GVD + GE+ G GAG++ + + L G+ AG Sbjct: 255 DGAPAITVRGLTV--PGWA--EGVDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAG 310 Query: 63 SIMVDGKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENV-MLGHEKRGPFGIDWK 118 ++ + G+P Q DA G+ + ++ L + + N+ ++ E+ +D Sbjct: 311 TVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALERYAKPWLDPA 370 Query: 119 KTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDAN 178 A ++ + + G+ + SS+S QQ +A+A+ + V++LDEPT +D Sbjct: 371 AEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVG 430 Query: 179 EVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIG 238 R+++ +++++ + G+A++ +S L ++ + R+ ++R G+ + +ELI Sbjct: 431 AKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIA 490 Query: 239 MMIG 242 G Sbjct: 491 HATG 494 Score = 84.7 bits (208), Expect = 7e-21 Identities = 61/214 (28%), Positives = 105/214 (49%), Gaps = 13/214 (6%) Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330 K G ++ V + G V G G G+G++ L ++L G + P +G ++G + Sbjct: 12 KEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGA---VR 68 Query: 331 DPYTALKNKIAYSTENRRDE-GIIGDLTVRQNILIALQATRGMF---KPIPKKEADAIVD 386 P + A E + DLT+ QNI + + RG+F K + +K +A+ Sbjct: 69 APGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTREALAK 128 Query: 387 KYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQ 446 + P DPD V+ L +Q V I R LA + LLI+DEPT + G + Sbjct: 129 VGL------PLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFA 182 Query: 447 VVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480 ++ L + G+ +++IS +L+EV R +D++ V++D Sbjct: 183 LMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRD 216 Lambda K H 0.316 0.135 0.376 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: 28 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 513 Length of database: 496 Length adjustment: 34 Effective length of query: 479 Effective length of database: 462 Effective search space: 221298 Effective search space used: 221298 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