GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proW in Pseudomonas fluorescens FW300-N2E3

Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate AO353_07785 AO353_07785 choline ABC transporter permease subunit

Query= SwissProt::P14176
         (354 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07785 AO353_07785 choline
           ABC transporter permease subunit
          Length = 281

 Score =  207 bits (527), Expect = 3e-58
 Identities = 107/263 (40%), Positives = 163/263 (61%), Gaps = 1/263 (0%)

Query: 62  IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121
           IPL  ++   ++W+  H    F  +   ++ +++G    L        I + AL+A  I 
Sbjct: 7   IPLGQYIAAFVEWLTQHGASTFDAIATTLETMIHGVTFALTWFNPLALIGLIALLAHFIQ 66

Query: 122 GV-GMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKII 180
              G+    + S + I  +G W + M TLA VL A   C++IG+PLGI  A  P    ++
Sbjct: 67  RKWGLTAFVIASFLLILNLGYWQETMETLAQVLFATFVCVIIGVPLGIVAAHKPMFYTMM 126

Query: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEA 240
           RP+LD MQT P FVYL+P + LFG+G VPG++ T++FA+   IRLT LGI  VP +L++A
Sbjct: 127 RPVLDLMQTVPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPQELMDA 186

Query: 241 SRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300
            ++FG S RQ+L +++LP AMP+I AG+ Q +ML+LSMVVIA+++   GLG+ V+  +  
Sbjct: 187 GKAFGCSRRQLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVNALNT 246

Query: 301 LDMGLATVGGVGIVILAIILDRL 323
            D+ L    G+ IV+LAI+LDR+
Sbjct: 247 ADIALGFEAGLAIVLLAIMLDRI 269


Lambda     K      H
   0.326    0.141    0.435 

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: 252
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: 354
Length of database: 281
Length adjustment: 27
Effective length of query: 327
Effective length of database: 254
Effective search space:    83058
Effective search space used:    83058
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 paper from 2022 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