Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 355 bits (910), Expect = e-102 Identities = 194/482 (40%), Positives = 293/482 (60%), Gaps = 13/482 (2%) Query: 4 KNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGS 63 + P++ M+GI F AL + LT+ PGE+HALMGENGAGKST++K L+GV+ + G Sbjct: 7 QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 66 Query: 64 IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHE 122 I++DG+P ++ AGI +YQE+ + N+SV NV +G E R G ID Sbjct: 67 ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 126 Query: 123 AAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182 L Q+G +SIA QQ V IARA+V ++++I+DEPT++L E Sbjct: 127 RTDAVLRQLGA-GFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQ 185 Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 LF ++R++RD G+AI+++SH + ++Y + DR+T+LR+G F+ E++ + + ++ MM+G Sbjct: 186 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 245 Query: 243 KSAAELSQIGAKKARREITPGEKP----IVDVKGLGKKGTINPVDVDIYKGEVVGFAGLL 298 +S +E Q + I P + ++ V+ L G I P D+ GEV+GFAGL+ Sbjct: 246 RSLSEFYQ------HQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLV 298 Query: 299 GSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTV 358 G+GRTEL RLL+GAD G L G+ V+I P A++ IAY E+R+ +G+ + V Sbjct: 299 GAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAV 358 Query: 359 RQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418 N + + + + + + ++ LNV+ A P+ PV LSGGNQQKVL+ R Sbjct: 359 AANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLAR 418 Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478 WL P++LILDEPTRG+DI AK+EI Q+V LASQG+ VV ISSEL EV+ + D + V+ Sbjct: 419 WLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVM 478 Query: 479 KD 480 ++ Sbjct: 479 RE 480 Score = 86.7 bits (213), Expect = 2e-21 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 9/201 (4%) Query: 33 GEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIATVYQE-- 90 GEV G GAG++ + + L G + G I+++G+P + A AGIA V ++ Sbjct: 289 GEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRK 348 Query: 91 -----VNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDPHTPLSSI 145 + + + NV H + G + + A+ + ++ ++ P TP+ + Sbjct: 349 GQGLFLQMAVAANATMNVASRHTRLGL--VRSRSLGGVARAAIQRLNVKVAHPETPVGKL 406 Query: 146 SIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLD 205 S QQ V +AR + I KVLILDEPT +D +++ ++ ++ GVA++ +S L Sbjct: 407 SGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELP 466 Query: 206 QIYEITDRLTILRNGQFIKEV 226 ++ I DR+ ++R G E+ Sbjct: 467 EVIGICDRVLVMREGMITGEL 487 Score = 75.9 bits (185), Expect = 3e-18 Identities = 61/244 (25%), Positives = 109/244 (44%), Gaps = 19/244 (7%) Query: 264 EKPIVDVKGLGKKG----TINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGT 319 + P++ ++G+ K ++ + + I GE+ G G+G++ L ++L G PD G Sbjct: 7 QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 66 Query: 320 YTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGM-----FK 374 L+G+ V + DP + I I +L V NI +A G Sbjct: 67 ILLDGRPVALRDPGASRAAGINL---------IYQELAVAPNISVAANVFMGSELRTRLG 117 Query: 375 PIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTR 434 I + D +++L D + LS QQ+V I R L ++I+DEPT Sbjct: 118 LIDHAAMRSRTDAVLRQLGAGFGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTA 176 Query: 435 GIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVS 494 + ++ VV L +G+ +++IS + EV L+D + VL+D + E+ D+ S Sbjct: 177 ALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS 236 Query: 495 QATI 498 + + Sbjct: 237 ERIV 240 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: 606 Number of extensions: 24 Number of successful extensions: 7 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: 502 Length adjustment: 34 Effective length of query: 479 Effective length of database: 468 Effective search space: 224172 Effective search space used: 224172 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