Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 340 bits (872), Expect = 7e-98 Identities = 185/480 (38%), Positives = 296/480 (61%), Gaps = 9/480 (1%) Query: 17 FPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGT 76 FPGV AL V L + PG V ALMGENGAGKST++K + G+Y+ +AG I + GKP F Sbjct: 33 FPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETP 92 Query: 77 LDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHEAAKKYLAQMGLES 135 L AQ AGIA ++QE+NL ++S+ EN+ +G E+ ++ ++ H + LA++ + + Sbjct: 93 LAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLARLRI-N 151 Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195 +DP + ++SIA +Q+V IA+A+ ++ +LI+DEPTS++ EV LF+I+ ++ G Sbjct: 152 LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGK 211 Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQIGAKK 255 I++++H +++++ I D + + R+G +I D LI MM+G+ ++L + Sbjct: 212 GIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFPL---- 267 Query: 256 ARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKP 315 RE TP ++ V+ L G V D++ GE++G AGL+GSGRT + ++G Sbjct: 268 --RE-TPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPS 324 Query: 316 DSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKP 375 SG TL+GK V ISDP+ A++ A TE+R+ G+ L+V +N+ +A+ Sbjct: 325 SSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGF 384 Query: 376 IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRG 435 I +K A+ + K+L V+ ++ + LSGGNQQK L+ RWL T+P LLILDEPTRG Sbjct: 385 IQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRG 444 Query: 436 IDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQ 495 ID+GAKAEI +++ LAS+GM V+ ISSEL EV+ +SD + V+ + + ++ + + Sbjct: 445 IDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQE 504 Score = 92.8 bits (229), Expect = 3e-23 Identities = 59/238 (24%), Positives = 119/238 (50%), Gaps = 6/238 (2%) Query: 271 KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNIS 330 KG + V + + G V+ G G+G++ L +++ G +PD+G L GK + Sbjct: 31 KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90 Query: 331 DPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMK 390 P A K IA ++ ++ +++ +NI I + + + +E + + Sbjct: 91 TPLAAQKAGIAMI---HQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCTAELLA 146 Query: 391 ELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLD 450 L + DP+ V NLS +Q V I + ++ ++LI+DEPT I A + ++ D Sbjct: 147 RLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIAD 205 Query: 451 LASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNVN 508 L SQG G+V+I+ ++ EV ++D++ V +D H I ++ D+++ +++ + ++ Sbjct: 206 LKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262 Score = 75.9 bits (185), Expect = 3e-18 Identities = 53/233 (22%), Positives = 116/233 (49%), Gaps = 11/233 (4%) Query: 23 LDGV----DLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLD 78 LDGV L+ GE+ + G G+G++ + + + G+ ++G I +DGK + + Sbjct: 284 LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHM 343 Query: 79 AQNAGIATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMG 132 A G A + ++ L LSV EN+ +L H F I K + ++ Sbjct: 344 AIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGF-IQQKALRALCEDMCKKLR 402 Query: 133 LESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRD 192 +++ + ++S QQ +AR ++ N ++LILDEPT +D +++ ++ + Sbjct: 403 VKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLAS 462 Query: 193 SGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 G+A++ +S L ++ ++DR+ ++ G+ + + + +++++ + G +A Sbjct: 463 EGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASGMTA 515 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: 623 Number of extensions: 28 Number of successful extensions: 8 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: 517 Length adjustment: 35 Effective length of query: 478 Effective length of database: 482 Effective search space: 230396 Effective search space used: 230396 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 Apr 09 2024. 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