GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Acidovorax sp. GW101-3H11

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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