Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_607 Predicted L-arabinose ABC transport system, ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_607 Length = 517 Score = 440 bits (1131), Expect = e-128 Identities = 228/486 (46%), Positives = 327/486 (67%), Gaps = 7/486 (1%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P++ + GI +F G+ L V L LYPGE+HALMG+NGAGKST+IK LTGV + + G + Sbjct: 17 PVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASGGQMR 76 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKR----GPFGIDWKKTH 121 + G+ + L AQ GI+TVYQEVNLC NLSV EN+ G R F IDW H Sbjct: 77 LGGQAVWPDSPLAAQRLGISTVYQEVNLCPNLSVAENIFAGRYPRCGIAQGFRIDWATLH 136 Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181 + A+ +A++GL+ ID LS +A+QQLVAIARA+ I ++VLILDEPTSSLD +EV+ Sbjct: 137 QRARDLVARIGLQ-IDVTRLLSDYPVAVQQLVAIARALSIESRVLILDEPTSSLDDDEVQ 195 Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 LF ++R++R G++I+FV+HFL+Q+Y ++DR+T+LRNG ++ E + KD LI M+ Sbjct: 196 KLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKDLGPQALIAAML 255 Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 G+ A S+ A + ++ +GLG+ + P+D+ I GEVVG AGLLGSG Sbjct: 256 GRDLAAASEQPAPAPA--VDSRHANLLQAEGLGQDTQLQPLDLQIRAGEVVGLAGLLGSG 313 Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361 RTEL RLL+G ++PD G ++G+ V ++P A+++ +A E R+ +GI+ +L+VR+N Sbjct: 314 RTELARLLFGLEQPDRGALRIDGQVVKFANPMDAIRHGLALCPEERKTDGIVAELSVREN 373 Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421 I +ALQA G+ K + + E + ++Y+K L ++ D+P+ LSGGNQQK ++ RW+A Sbjct: 374 IALALQARMGVGKFLSRSEQTELAERYVKLLGIKTETVDKPIGLLSGGNQQKAILARWMA 433 Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDR 481 P LLILDEPTRGID+ AK EI +L LA GM V+FISSE+ EVVR++ I VL+DR Sbjct: 434 IEPRLLILDEPTRGIDVAAKQEIMDQILRLAQAGMAVLFISSEMSEVVRVAHRIVVLRDR 493 Query: 482 HKIAEI 487 K+ E+ Sbjct: 494 RKVGEL 499 Score = 74.3 bits (181), Expect = 1e-17 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 18/247 (7%) Query: 262 PGEKPIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDS 317 P P++ + G+ K+ + V +++Y GE+ G G+G++ L ++L G + Sbjct: 13 PAAAPVLQLSGIHKQFAGITVLRDVQLNLYPGEIHALMGQNGAGKSTLIKVLTGVLEASG 72 Query: 318 GTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIP 377 G L G+ V P A ++ ST + + + +L+V +NI G+ + Sbjct: 73 GQMRLGGQAVWPDSPLAA--QRLGISTVYQ-EVNLCPNLSVAENIFAGRYPRCGIAQGFR 129 Query: 378 ------KKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDE 431 + A +V + +++V D PV QQ V I R L+ +LILDE Sbjct: 130 IDWATLHQRARDLVARIGLQIDVTRLLSDYPV-----AVQQLVAIARALSIESRVLILDE 184 Query: 432 PTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDD 491 PT +D ++ +V+ L S+G+ +VF++ L +V +SD I VL++ + E D Sbjct: 185 PTSSLDDDEVQKLFEVLRRLRSEGLSIVFVTHFLNQVYAVSDRITVLRNGSWVGEWLAKD 244 Query: 492 TVSQATI 498 QA I Sbjct: 245 LGPQALI 251 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: 637 Number of extensions: 25 Number of successful extensions: 8 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: 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 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