GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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