Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20250 Length = 514 Score = 314 bits (805), Expect = 4e-90 Identities = 178/482 (36%), Positives = 290/482 (60%), Gaps = 12/482 (2%) Query: 12 GITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ 71 GI FPGV+AL + +PG+VHALMGENGAGKST++K L G Y ++G + + + Sbjct: 20 GIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTM 79 Query: 72 QFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQM 131 F GT D+ +G+A ++QE++L ++V EN+ LGH FG+ + L + Sbjct: 80 AFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLP-ARFGLVNRGVLRQQALTLLKG 138 Query: 132 GLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVR 191 + IDP + +S+ +QLV IA+A+ A V+ DEPTSSL A E+ L AI+ ++R Sbjct: 139 LADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIARLR 198 Query: 192 DSGVAILFVSHFLDQIYEITDRLTILRNGQFIK--EVMTKDTPRDELIGMMIGKSAAELS 249 D G +L+VSH +++++ I + +T+ ++G++++ E M++ T D+L+ M+G+ ++ Sbjct: 199 DEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT-HDQLVTCMVGRDIQDIY 257 Query: 250 QIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLL 309 ++ R ++ + VK L G PV ++KGE++G GL+G+GRTEL RLL Sbjct: 258 DYRPRE-RGDVA------LQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLL 310 Query: 310 YGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQAT 369 G ++ G+ L+GK++ + P A+ + E+R+ EGII +V +NI I+ + Sbjct: 311 SGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPA 370 Query: 370 RGMFKPIPKKEAD-AIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLI 428 + + + + DK +K L V+ + + LSGGNQQK ++GRWL+ ++L+ Sbjct: 371 HSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLL 430 Query: 429 LDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIE 488 LDEPTRGIDIGAKAEI Q++ +LA+ G+ V+ +SS+L EV+ +SD I VL + E+ Sbjct: 431 LDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELS 490 Query: 489 ND 490 D Sbjct: 491 RD 492 Score = 78.6 bits (192), Expect = 5e-19 Identities = 62/241 (25%), Positives = 115/241 (47%), Gaps = 30/241 (12%) Query: 18 PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTL 77 PG++ + V ++ GE+ L G GAG++ + + L+G+ + + GS+++ GK + Sbjct: 277 PGLR--EPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLHGKELKLRSPR 334 Query: 78 DAQNAGIATVYQE---VNLCTNLSVGENV---------MLGHEKRGPFGIDWKKTHEAAK 125 DA AG+ ++ + SVGEN+ LG RG DW++ + Sbjct: 335 DAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRG----DWERGN---- 386 Query: 126 KYLAQMGLESIDPHTPLSS-----ISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEV 180 A ++S+ TP +S +S QQ + R + + KVL+LDEPT +D Sbjct: 387 ---ADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAK 443 Query: 181 RDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMM 240 +++ I+ + G+A++ VS L ++ I+DR+ +L G E+ L+ + Sbjct: 444 AEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLA 503 Query: 241 I 241 + Sbjct: 504 L 504 Score = 65.9 bits (159), Expect = 3e-15 Identities = 49/223 (21%), Positives = 104/223 (46%), Gaps = 10/223 (4%) Query: 287 YKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTEN 346 + G+V G G+G++ L ++L GA P SG + + + ++ + +A + Sbjct: 39 HPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQE 98 Query: 347 RRDEGIIGDLTVRQNILIA-LQATRGMF-KPIPKKEADAIVDKYMKELNVRPADPDRPVK 404 ++ ++TV +N+ + L A G+ + + +++A ++ E+ DP V Sbjct: 99 LH---LVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTLLKGLADEI-----DPQEKVG 150 Query: 405 NLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSE 464 LS G +Q V I + L+ ++ DEPT + + ++ L +G V+++S Sbjct: 151 RLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIARLRDEGKVVLYVSHR 210 Query: 465 LEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETIANTNV 507 +EEV R+ + + V KD + EN ++ +V + ++ Sbjct: 211 MEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDI 253 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: 605 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: 514 Length adjustment: 35 Effective length of query: 478 Effective length of database: 479 Effective search space: 228962 Effective search space used: 228962 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