Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 448 bits (1153), Expect = e-130 Identities = 236/506 (46%), Positives = 339/506 (66%), Gaps = 2/506 (0%) Query: 2 TDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA 61 T P++ ++G++ F GV+ALDGVD T+ GE+HAL+GENGAGKST+IK LTGVY+ +A Sbjct: 7 TASPPLLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDA 66 Query: 62 GSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH 121 G++ ++G+ G +AQ I TVYQEVNL NLSV EN+ LG + +D Sbjct: 67 GTVTLEGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMR 126 Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181 A+ L GL ++D PL S+A QQ+VAIARA+ ++AKVLILDEPT+SLDA EV Sbjct: 127 RRARAVLIPYGL-TLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVA 185 Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 LF +MR +R G+ I+FV+HFLDQ+Y + DR+T+LRNG+ + E T + PR +L+ MM+ Sbjct: 186 VLFKVMRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMML 245 Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 G+ ++ A A P+V +G GK ++ P D+DI GEVVG AGLLGSG Sbjct: 246 GRELEAVAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSG 305 Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361 RTE RL++G D+ D G ++G+ V + P A++ + E+R+ EGI+G L+VR+N Sbjct: 306 RTETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVREN 365 Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421 I++ALQA +G +PIP+ + I D++++ L++R ++P++ LSGGNQQK L+ RWLA Sbjct: 366 IILALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLA 425 Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDR 481 T P LLILDEPTRGID+GA AEI +++ L + GM ++ +SSELEE+V S + VL+DR Sbjct: 426 TEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDR 485 Query: 482 HKIAEIENDDTVSQATIVETIANTNV 507 +AE+ + V+ IV IA+ +V Sbjct: 486 RHVAELRGGE-VAVDRIVAAIASESV 510 Score = 89.0 bits (219), Expect = 4e-22 Identities = 60/247 (24%), Positives = 121/247 (48%), Gaps = 9/247 (3%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P+V +G + ++++ DL + PGEV L G G+G++ + + G+ + + G Sbjct: 270 PLVRFRG----YGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAA 325 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEKRGPF--GIDWKKT 120 VDG+ + G DA G ++ + LSV EN++L + R + I + Sbjct: 326 VDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQARQGWLRPIPRCRQ 385 Query: 121 HEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEV 180 E A +++ + + + P+ +S QQ +AR + ++LILDEPT +D Sbjct: 386 EEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGAH 445 Query: 181 RDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMM 240 ++ ++ ++ G+A+L VS L++I + R+ +LR+ + + E+ + D ++ + Sbjct: 446 AEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAAI 505 Query: 241 IGKSAAE 247 +S E Sbjct: 506 ASESVPE 512 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: 693 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 516 Length adjustment: 35 Effective length of query: 478 Effective length of database: 481 Effective search space: 229918 Effective search space used: 229918 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