GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1748 in Pseudomonas fluorescens FW300-N2E2

Align TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate Pf6N2E2_3231 Dipeptide transport system permease protein DppC (TC 3.A.1.5.2)

Query= TCDB::Q9X270
         (289 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3231
          Length = 300

 Score =  179 bits (453), Expect = 9e-50
 Identities = 96/271 (35%), Positives = 149/271 (54%), Gaps = 1/271 (0%)

Query: 18  LRFK-KNKMAVIGGVFVLILIALAILAPYIAPYPYDEPHYIRAFEGPSKDFIFGTDALGR 76
           LRF  +N M   G + V  L+ +A+ AP+IA +     +   A + PS    FGTD  GR
Sbjct: 29  LRFLLRNPMTFAGLIVVATLMLVAVFAPWIAGHDPLLQNLAGALQAPSGVHWFGTDEYGR 88

Query: 77  DLFSRILYSLRNACIIGFGSQFVVLIIGGILGAVAGFKGGWIDKFIMSIVDIMFAFPTFL 136
           D+F+R++Y  R    I      +V  IG ++G V+G+ GGW+D   M I DI  +FP+ +
Sbjct: 89  DVFARLVYGSRITLYIVLLVTVIVGPIGLLVGTVSGYFGGWVDSLFMRITDIFISFPSLV 148

Query: 137 FNVILVTALGRGLFTIFLAIGLTGWAGMARLVRGQVLYLKNSEFVEAAKAAGASTFYIIR 196
             +  + ALG GL    +AI LT W  +ARL R + L L+N++FV A +  GAS+  II 
Sbjct: 149 LALAFIAALGPGLEHAVIAIALTAWPPIARLARAETLPLRNADFVVAVQLQGASSTRIIL 208

Query: 197 KHILPNMIGPILVNLAFGVPGAMMTESGLAVIGMGVRPPMPSWGNLIGEGIGMMMAFPHL 256
           +HI+P  +  +++ L   +   ++T + L  +G+G + P+P WG +I  G   M+    L
Sbjct: 209 RHIIPMCLSSVIIRLTMNMASIILTAAALGFLGLGAQAPLPEWGAMISTGRRYMLESWWL 268

Query: 257 LIFPAVTFAFTLISFTFLADGLRDAFNPRSE 287
           +  P        ++F  L DGLRD  +PRS+
Sbjct: 269 VAAPGAAIMLVSLAFNLLGDGLRDVLDPRSQ 299


Lambda     K      H
   0.331    0.147    0.457 

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: 199
Number of extensions: 9
Number of successful extensions: 1
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: 289
Length of database: 300
Length adjustment: 26
Effective length of query: 263
Effective length of database: 274
Effective search space:    72062
Effective search space used:    72062
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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