GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Acidovorax sp. GW101-3H11

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  272 bits (696), Expect = 2e-77
 Identities = 175/475 (36%), Positives = 255/475 (53%), Gaps = 9/475 (1%)

Query: 15  VEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFS 74
           VE   VTK FG    L+ V   + PG  + L+G NGAGKSTL+ IL G   P TGEV   
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64

Query: 75  GAA-APSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133
           GA  AP    R A  + +  ++Q   +  DL++A+N+F+  +  RG  +D +AMR   R 
Sbjct: 65  GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTRE 124

Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193
            L    + +  D R   L V  +QLVEIARAL+  AR +I+DEPTA L   E +RLF  +
Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184

Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253
           + L+  GVT ++ISH L EV      V V+RD   +     +++ R Q+   M G     
Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRE--- 241

Query: 254 AVADA-AARGALPADTAVALELKELTGADY-EGVSFTVKRGEVVGLTGATSSGRTSVAEA 311
            +AD    +   P D A A+ ++ LT   + EGV F V+RGE++G  G   +GRT + E 
Sbjct: 242 -LADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELFEG 300

Query: 312 IAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371
           + GLR    GT+ + G  +       +  HG+  + +DR  +GL +   +  N ++    
Sbjct: 301 LLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMALE 360

Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431
              K  +  PA + A  ++ +   GI     E   S LSGGNQQK+ +A+ L   P+V+V
Sbjct: 361 RYAKPWL-DPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVV 419

Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDL-RTCDRVLVMFRGRV 485
           L +PT GVDV +K  +  +V R+ E+G AV+V+S EL +L   C RV VM  GR+
Sbjct: 420 LDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRL 474



 Score = 65.5 bits (158), Expect = 4e-15
 Identities = 63/232 (27%), Positives = 96/232 (41%), Gaps = 23/232 (9%)

Query: 33  VSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRERVA 92
           V   V  GE     G  GAG++ L   L GLR    G V  +G      + RDA R  + 
Sbjct: 274 VDFEVRRGEILGFAGLVGAGRTELFEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLT 333

Query: 93  CVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHW--KIDVRE------ 144
            + +     + L V   L  N        +   A+ R A+  LD    +  +RE      
Sbjct: 334 YLSEDRKG-KGLHVHFGLRPN--------LTLMALERYAKPWLDPAAEQAALREAVQEFG 384

Query: 145 ------DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198
                 + RA  LS   +Q + +A+ L  G   ++LDEPT  +D    + ++  +  L  
Sbjct: 385 IRTGSLEVRASSLSGGNQQKLALAKVLHPGPSVVVLDEPTRGVDVGAKREIYHLVQRLAE 444

Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGER 250
           +G+  + IS  L E+  +C  V V+R  R   +     L  E+LI   TG R
Sbjct: 445 QGLAVIVISSELMELIGLCHRVAVMRAGRLQTTLQEPHLTEEELIAHATGTR 496


Lambda     K      H
   0.318    0.134    0.377 

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: 579
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 496
Length adjustment: 34
Effective length of query: 476
Effective length of database: 462
Effective search space:   219912
Effective search space used:   219912
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 (21.7 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