GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacJ in Pseudomonas fluorescens FW300-N2C3

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate AO356_00010 AO356_00010 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00010 AO356_00010 ABC
           transporter ATP-binding protein
          Length = 365

 Score =  256 bits (654), Expect = 7e-73
 Identities = 147/372 (39%), Positives = 211/372 (56%), Gaps = 20/372 (5%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  +++ +L K F     +  + L++ D+EF+V VGPSGCGKST LR++AGLE  TSG I
Sbjct: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120
            + G  +    P  RD+AMVFQ YALYPHMTVR+N+ F L+   G    + + +V E A 
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLA-GEKKPDVERKVAEAAR 119

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            L +  LLDRKP +LSGGQ+QRVA+GRAIVR+P++FL DEPLSNLDA LR + R EL  L
Sbjct: 120 ILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRL 179

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
             +L  T +YVTH+Q EAMT+A ++ V++ G ++Q+ SP E YH P NLFVA F+G P +
Sbjct: 180 HKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKM 239

Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDR-----DDFVLGVRPEDIEVADAAPDDAA 295
             ++ T       G    +     ++   D           +G+RPE + +         
Sbjct: 240 GFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLG-------- 291

Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355
             +  + +   V E  G     H++      + ++L    +G   V    R  +T+    
Sbjct: 292 -AEGQVLVTTDVTERLGSDTFCHVN----VDSGESLTVRVQGDCEVPYAARRYLTLDVAH 346

Query: 356 IHLFDAETGTAV 367
            HLFD E+G +V
Sbjct: 347 CHLFD-ESGLSV 357


Lambda     K      H
   0.317    0.135    0.386 

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: 326
Number of extensions: 13
Number of successful extensions: 2
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: 383
Length of database: 365
Length adjustment: 30
Effective length of query: 353
Effective length of database: 335
Effective search space:   118255
Effective search space used:   118255
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 (21.6 bits)
S2: 50 (23.9 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 preprint 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