GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Pseudomonas fluorescens GW456-L13

Align Fructose import permease protein FrcC (characterized)
to candidate PfGW456L13_2122 L-arabinose transport system permease protein (TC 3.A.1.2.2)

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2122
          Length = 323

 Score =  136 bits (343), Expect = 7e-37
 Identities = 94/306 (30%), Positives = 153/306 (50%), Gaps = 20/306 (6%)

Query: 56  VLSLIAFGV-----ILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110
           V+ L A G+     +L   F S   M  +   ++  GI        + +   DLSVG+++
Sbjct: 26  VMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVI 85

Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170
             + V+      R      L V   L +G + G ING ++A++++   I TL   QIV  
Sbjct: 86  ACAGVVAA-VVMRDTNSVFLGVCAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRG 144

Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNA-VFTYGVVVMVLLVCLLWY--VLNR 227
             ++++  + +     S            F  GN  +F   V +++ +VC L++  +LN 
Sbjct: 145 LAYIFANGKAVGVSQESF-----------FVFGNGQMFGVPVPILITIVCFLFFGWLLNY 193

Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287
           T +GR   A+G + EAA LAGVNV R  I I+ + G+I ALAG  L  R+ S  P  GQ 
Sbjct: 194 TTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQG 253

Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347
             +  I+A V+GG+SL GG G I  ++ G LI+ +    + L   D  + Y++ G ++++
Sbjct: 254 FELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLL 313

Query: 348 AVAIDQ 353
           AV ID+
Sbjct: 314 AVVIDR 319


Lambda     K      H
   0.327    0.141    0.420 

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: 316
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 360
Length of database: 323
Length adjustment: 29
Effective length of query: 331
Effective length of database: 294
Effective search space:    97314
Effective search space used:    97314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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