GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Pseudomonas fluorescens FW300-N2C3

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20250
          Length = 514

 Score =  345 bits (886), Expect = 2e-99
 Identities = 192/504 (38%), Positives = 305/504 (60%), Gaps = 19/504 (3%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           LR  G+ K FPGV+AL N+ F    G++ AL+GENGAGKSTL+K L G Y    G + + 
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
            Q ++ K TA +   G+  ++QE++L+P M+VA+NLF+G  P RFGL+ R  + ++A  L
Sbjct: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      +D +E + R S+  +Q+V I +A+   A V+  DEPT+SL  +E++ L  ++ 
Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIA 195

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRET-CELPQIELVKMMLGRELD- 247
           +LRD G  +++V+H +++V+++ + +TV ++G +V   E   EL   +LV  M+GR++  
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQD 255

Query: 248 --THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305
              +  +  G   L  K +         G   P   +V  GEI+GL GL+G+GRTE   +
Sbjct: 256 IYDYRPRERGDVALQVKSLLG------PGLREPVSFQVHKGEILGLFGLVGAGRTELFRL 309

Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           + G++    G+ ++ GK   LRSP  A   G+  CPEDRK +GII   SV ENI ++ + 
Sbjct: 310 LSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARP 369

Query: 366 QRGWLRPISRKE-QQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424
               L  + R + ++  A++ I+ L ++TP+  Q I +LSGGNQQK +L RWL    + L
Sbjct: 370 AHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVL 429

Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD------- 477
           +LDEPTRGID+GA AEI ++I  L ADG+A++V+SS+L E++G +DR++++ +       
Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489

Query: 478 -RKQVAEIPLAELSVPAIMNAIAA 500
            R Q  E  L +L++P    A AA
Sbjct: 490 SRDQANESNLLQLALPRQRVADAA 513


Lambda     K      H
   0.321    0.138    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: 591
Number of extensions: 33
Number of successful extensions: 7
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: 500
Length of database: 514
Length adjustment: 34
Effective length of query: 466
Effective length of database: 480
Effective search space:   223680
Effective search space used:   223680
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 (21.8 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