Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 314 bits (805), Expect = 4e-90 Identities = 178/513 (34%), Positives = 306/513 (59%), Gaps = 22/513 (4%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA--GSI 64 ++ M+ I FPGV AL+ V+L + GE+HA++GENGAGKST++K L+GVY + G I Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 65 MVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAA 124 + DG+ ++F G D+++ GI ++QE+ L LS+ EN+ LG+E IDW H A Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRA 121 Query: 125 KKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLF 184 + L ++GL P TP+ + + QQLV IA+A+ ++LILDEPT+SL+ N+ + L Sbjct: 122 QALLHKVGLGE-SPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALL 180 Query: 185 AIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTP--RDELIGMMIG 242 ++ +++ G+ + +SH L++I + D +T+LR+G ++ + ++ P D +I M+G Sbjct: 181 DLLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVG 240 Query: 243 KSAAELSQIGAKKARREITPGEKPIVDVKGL-------GKKGTINPVDVDIYKGEVVGFA 295 + ++ + +R+ GE + +V+ + + +D+++ +GE+VG A Sbjct: 241 REMSD------RYPQRQPQVGEI-VFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIA 293 Query: 296 GLLGSGRTELGRLLYGAD--KPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGII 353 GL+G+GRTEL ++G + SG L+G+ +++S A+ + +AY TE+R+ G++ Sbjct: 294 GLMGAGRTELAMSIFGRSWGQRISGEVRLHGQPIDVSTVEKAVSHGLAYVTEDRKGNGLV 353 Query: 354 GDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQK 413 + ++ N +A I + + Y ++L +R + D+ NLSGGNQQK Sbjct: 354 LNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYREKLRIRCSGVDQKTLNLSGGNQQK 413 Query: 414 VLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSD 473 V++ +WL T PE+LILDEPTRGID+GAK EI ++ LA++G V+ ISSE+ E++ ++D Sbjct: 414 VVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPELLGITD 473 Query: 474 DIEVLKDRHKIAEIENDDTVSQATIVETIANTN 506 I V+ + +AE+ + SQ I+ I + Sbjct: 474 RIYVMNEGRFVAEMPTSE-ASQEKIMRAIVKAS 505 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: 635 Number of extensions: 36 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 513 Length of database: 505 Length adjustment: 34 Effective length of query: 479 Effective length of database: 471 Effective search space: 225609 Effective search space used: 225609 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