Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 311 bits (796), Expect = 4e-89 Identities = 177/493 (35%), Positives = 283/493 (57%), Gaps = 10/493 (2%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 + FR + K F V+ L + F G+V+ L+GENGAGKSTL+KIL+G +PTTG VV++ Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 68 GQEMSFSDTTAALNA-GVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGL 126 G + + A A G+ +I+QE +L ++T+A+NI+LG +G ++ + + Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTRE 124 Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 L +G+ +DPDT ++ L + + Q+VEIA+ALARNA+++ DEPT++L+ E + LF ++ Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 L+ G I+Y+SH+++E+ +D + V +DG V V + MVGR++ Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAR-EATASVTRRQMANLMVGRELA 243 Query: 247 DIYGWQPR----SYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 D++ P+ G + + + PG + VR GEI+G GLVGAGR+EL +G+ Sbjct: 244 DLF--PPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEGL 301 Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362 G TAG V I QP+ ++ P A G+ EDRK +G+ +R N+ + A + Sbjct: 302 LGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALER 361 Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422 + ++ E+ ++ I+T E +LSGGNQQK L + L V++ Sbjct: 362 YAKPW--LDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVV 419 Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482 LDEPTRG+DVGAK EIY+++ LA QG+AV+ SS+L E++G+ R+ VMR G + L Sbjct: 420 LDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQ 479 Query: 483 HEQADERQALSLA 495 E + ++ A Sbjct: 480 EPHLTEEELIAHA 492 Lambda K H 0.319 0.136 0.391 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: 607 Number of extensions: 34 Number of successful extensions: 8 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: 504 Length of database: 496 Length adjustment: 34 Effective length of query: 470 Effective length of database: 462 Effective search space: 217140 Effective search space used: 217140 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 (21.7 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