Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 277 bits (709), Expect = 6e-79 Identities = 174/496 (35%), Positives = 273/496 (55%), Gaps = 21/496 (4%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ MK I EFPG+ A D V L + GE+HAL+GENGAGKST++ L G+Y+ G I+V Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126 GKP + A GI V+Q L +V EN++LG E I+ KK +A + Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 Q GL ++DP+ + IS+ MQQ V I + + A++LI DEPT++L E+ +L I Sbjct: 124 ISKQYGL-AVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS-- 244 M+K+ G +I+ ++H L +I E+ DR T++R G+ I V ++ D L MM+G+ Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242 Query: 245 -AAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303 + E K A +I K +V VK +N + ++++ GE++G AG+ G+G+T Sbjct: 243 FSVEKDPAQPKDAVLQI----KDLV-VKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQT 297 Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363 EL + G KP G LNG+ + P + + ++R G++ D TV +NI+ Sbjct: 298 ELIEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357 Query: 364 IAL-----QATRGM--FKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLI 416 + +T G+ F I KK A+ +++ Y +VR + LSGGNQQK +I Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKK-ANELIEDY----DVRTPSEHTLARALSGGNQQKAII 412 Query: 417 GRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIE 476 R + P+LLI +PTRG+D+GA I ++ +G V+ IS EL+EV+ +SD I Sbjct: 413 AREVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIA 472 Query: 477 VLKDRHKIAEIENDDT 492 V+ + +A ++ D T Sbjct: 473 VIYEGKIVAIVDADKT 488 Score = 95.1 bits (235), Expect = 5e-24 Identities = 62/250 (24%), Positives = 130/250 (52%), Gaps = 8/250 (3%) Query: 4 KNPIVVMKGITI-EFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62 K+ ++ +K + + + + A++ + L ++ GE+ + G +G G++ +I+A+TG+ K G Sbjct: 253 KDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGG 312 Query: 63 SIMVDGKPQQFNGTLDAQNAGIATVYQEVN---LCTNLSVGENVMLGHEKRGPFG----I 115 +I ++G+ AG+ + Q+ + L + +VGEN++L + P+ + Sbjct: 313 NIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVL 372 Query: 116 DWKKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSL 175 ++ + ++ A + + + + HT ++S QQ IAR + + +LI +PT L Sbjct: 373 NFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGL 432 Query: 176 DANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE 235 D + + + K RD G A+L +S LD++ ++DR+ ++ G+ + V T +E Sbjct: 433 DVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENE 492 Query: 236 LIGMMIGKSA 245 L +M G SA Sbjct: 493 LGLLMAGGSA 502 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: 685 Number of extensions: 44 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 513 Length of database: 509 Length adjustment: 35 Effective length of query: 478 Effective length of database: 474 Effective search space: 226572 Effective search space used: 226572 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