GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Pseudomonas fluorescens FW300-N2E2

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf6N2E2_3426 Peptide ABC transporter, ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3426
          Length = 323

 Score =  179 bits (453), Expect = 1e-49
 Identities = 110/297 (37%), Positives = 173/297 (58%), Gaps = 15/297 (5%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           A+  VSLS+  G++L ++GESG+GK+TLGR I+ L + ++G++++DG ++ + KR   ++
Sbjct: 30  AVNGVSLSLAPGEVLGLVGESGSGKSTLGRAILRLTEVSAGQILFDGVDMAQGKRIDIER 89

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE-KINKDELRKRLINLLELVKLTPAEE 145
            R +  +I QDPY+ L    ++ + L A +LR    I    +R+R+  LL LV L P  E
Sbjct: 90  LRHETAMIFQDPYTALNPRMSIGDTL-AEVLRVRCAIPASLIRQRVDELLNLVGLRP--E 146

Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205
              + P  LSGGQ QR+ IAR+L++ PR+I+ADE V  +D S++  I+N L E++ R+NL
Sbjct: 147 LADRKPGSLSGGQCQRVGIARALAIEPRLIIADECVAALDVSIQGQIINLLLELRQRMNL 206

Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSI 265
            ++FI HD+ I R    L D+    VM+ G IVE+   E +  +P HPYT  LI+  P I
Sbjct: 207 AILFIAHDLAIVR---RLCDR--VAVMYLGEIVEQGPTEAVFSNPRHPYTVALIQSIPHI 261

Query: 266 DNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKYS-HEVACFL 316
           D     ++  +  E      +  GC +  RC +A  IC    P +   + H  +C L
Sbjct: 262 DPTRPLLSAPLPGEPPSPLNLPSGCAFHPRCRYAQPICAKTPPPIHDINGHRYSCVL 318


Lambda     K      H
   0.321    0.141    0.410 

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: 295
Number of extensions: 12
Number of successful extensions: 4
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: 324
Length of database: 323
Length adjustment: 28
Effective length of query: 296
Effective length of database: 295
Effective search space:    87320
Effective search space used:    87320
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: 48 (23.1 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