Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF2651 PGA1_c26910 ABC transporter, ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Phaeo:GFF2651 Length = 522 Score = 260 bits (664), Expect = 1e-73 Identities = 157/478 (32%), Positives = 256/478 (53%), Gaps = 9/478 (1%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ ++ IT F V A D V L+PGEV AL+GENGAGK+T++ L G Y + G + Sbjct: 14 PVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADTGGVE 73 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 + G P A + G+ V+Q L NL+V EN+ LG E G+ + Sbjct: 74 LFGAPLPPGAPRAALDGGVGMVHQHFTLADNLTVWENITLGVEPLLGLGLRAGPAKARIR 133 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 Q L+ +DP+ +S +++ +Q V I +A+ +A++LILDEPT+ L E LFA Sbjct: 134 ALAEQFHLK-VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLTPQESDALFA 192 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 +R+ + G++++F+SH L ++ I+DR+ +LR+G+ + E T DT D L +M+G Sbjct: 193 TLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDALAALMVGADV 252 Query: 246 AELSQIGAKKARREITPGEKPIVDV--KGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 + AK A P + DV G + V +D+ G++ G AG+ G+G+ Sbjct: 253 -----VPAKFAANTPGPALLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQA 307 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 L L+ G P SG+ TLNG P A+ IA E+R G I D + +N + Sbjct: 308 ALSDLVSGLITPQSGSLTLNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAI 367 Query: 364 IALQATRGMFKP-IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422 + ATR + + + A + +VR PD ++ LSGGN QK+++GR L Sbjct: 368 LETYATRFSHRGWLDWRAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQ 427 Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480 P++++ ++P RG+DIGA + + + ++G V+ IS +L+E+++LSD I V+ + Sbjct: 428 SPQIILANQPVRGLDIGAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISE 485 Score = 87.8 bits (216), Expect = 9e-22 Identities = 66/239 (27%), Positives = 122/239 (51%), Gaps = 10/239 (4%) Query: 262 PGEKPIVDVKGLGKK-GTI---NPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDS 317 PG P++ ++ + K+ G++ + V D++ GEV+ G G+G+T L +L+G D+ Sbjct: 10 PGLTPVLRLQNITKRFGSVTANDDVSFDLFPGEVIALLGENGAGKTTLMNILFGQYMADT 69 Query: 318 GTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP 377 G L G + P AL + ++ + +LTV +NI + ++ G+ + Sbjct: 70 GGVELFGAPLPPGAPRAALDGGVGMVHQHFT---LADNLTVWENITLGVEPLLGL--GLR 124 Query: 378 KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437 A A + ++ +++ DP+ V L+ G +Q+V I + L +LILDEPT + Sbjct: 125 AGPAKARIRALAEQFHLK-VDPNAKVSRLTVGERQRVEILKALYRDARILILDEPTAVLT 183 Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQA 496 + + + ++G+ V+FIS +L EV+ +SD + VL+ +AE + DT S A Sbjct: 184 PQESDALFATLREAINRGLSVIFISHKLHEVMAISDRVLVLRHGKLVAERQTADTDSDA 242 Score = 65.9 bits (159), Expect = 3e-15 Identities = 52/245 (21%), Positives = 107/245 (43%), Gaps = 11/245 (4%) Query: 7 IVVMKGITIEFPGVK-ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 ++ ++ +T G L V L L G++ L G +G G++ + ++G+ +GS+ Sbjct: 266 LLQLRDVTTPSAGASPGLRHVSLDLAAGQITGLAGVSGNGQAALSDLVSGLITPQSGSLT 325 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLG-----HEKRGPFGIDW 117 ++G +A AGIA + ++ + + EN +L RG +DW Sbjct: 326 LNGAAPAGWSPREAITAGIARIPEDRHKTGTIADFDLTENAILETYATRFSHRG--WLDW 383 Query: 118 KKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDA 177 + + AK + + P T + +S Q + + R + + ++++ ++P LD Sbjct: 384 RAARDFAKTVITGYDVRCPGPDTRIRLLSGGNMQKLILGRVLEQSPQIILANQPVRGLDI 443 Query: 178 NEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237 V + + K G A+L +S LD+I +++D + ++ G+ +EL Sbjct: 444 GAVTYVHEQLAKACARGAAVLLISEDLDEIMQLSDVIHVISEGRLSPGFARGSKQPEELG 503 Query: 238 GMMIG 242 M G Sbjct: 504 AWMAG 508 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: 609 Number of extensions: 35 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: 522 Length adjustment: 35 Effective length of query: 478 Effective length of database: 487 Effective search space: 232786 Effective search space used: 232786 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