Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate Ac3H11_609 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_609 Length = 505 Score = 348 bits (894), Expect = e-100 Identities = 210/518 (40%), Positives = 306/518 (59%), Gaps = 30/518 (5%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71 LL +RNI KTFPGV AL +V L AGE+HA++GENGAGKSTLMK+LSG Y G+ Sbjct: 2 LLEMRNIRKTFPGVVALNQVNLQVQAGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGQI 61 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 DGQ + G + + LG+ +I+QEL+L P LS+AENI+LG R G++ Sbjct: 62 LFDGQEREFAGIRDSEHLGIIIIHQELALVPLLSIAENIFLGNETARHGVIDWMAAHSRA 121 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 L ++G SP V L + ++QLVEIA+A+ + R+L++DEPT L+ +++ L Sbjct: 122 QALLHKVGLGESPDTPVGQLGVGKQQLVEIAKALSRKVRLLILDEPTASLNENDSQALLD 181 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD--RAHLSQAALVKMMVGR 249 L+ +L+ +G+ + ISH++ EI +AD +TVLRDG V LD +S+ +++ MVGR Sbjct: 182 LLLELKAQGITCILISHKLNEISRVADAITVLRDGSTVQMLDCREGPVSEDRVIQAMVGR 241 Query: 250 DLSGFYTKTHGQAVEREVMLSVRDV-------ADGRRVKGCSFDLRAGEVLGLAGLVGAG 302 ++S Y + Q E++ VR+ +D +KG ++R GE++G+AGL+GAG Sbjct: 242 EMSDRYPQRQPQV--GEIVFEVRNWRAHHPQRSDREHLKGIDLNVRRGEIVGIAGLMGAG 299 Query: 303 RTELARLVFGAD--ARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL 360 RTELA +FG R GEVR+ + +A+ G+AY+TEDRK GL Sbjct: 300 RTELAMSIFGRSWGQRISGEVRLHGQP-------IDVSTVEKAVSHGLAYVTEDRKGNGL 352 Query: 361 FLDQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALS 416 L++ + N +L V+ + G+ +R A R + L IR + LS Sbjct: 353 VLNEDIQFNTSLANLPGVSFASVIDSGQEHRVAQDYR-----EKLRIRCSGVDQKTLNLS 407 Query: 417 GGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPE 476 GGNQQKV+LS+ L P VLILDEPTRG+D+GAK EIY LI LA G +++ISSE+PE Sbjct: 408 GGNQQKVVLSKWLFTSPEVLILDEPTRGIDVGAKYEIYTLIAQLAAEGKCVIVISSEMPE 467 Query: 477 VVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALAT 514 ++G+ DR+ VM EG E+ + ++ E R I A+ Sbjct: 468 LLGITDRIYVMNEGRFVAEMPTSEASQEKIMRAIVKAS 505 Lambda K H 0.320 0.136 0.382 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: 591 Number of extensions: 33 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: 540 Length of database: 505 Length adjustment: 35 Effective length of query: 505 Effective length of database: 470 Effective search space: 237350 Effective search space used: 237350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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