GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Pseudomonas fluorescens FW300-N1B4

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate Pf1N1B4_3744 ABC transporter, ATP-binding protein

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3744
          Length = 329

 Score =  265 bits (678), Expect = 1e-75
 Identities = 136/279 (48%), Positives = 192/279 (68%), Gaps = 2/279 (0%)

Query: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77
           V +  ++K + G  V   ++  I  GEF+TLLGPSGCGK+T+LR IAGL +VD G+I+L+
Sbjct: 4   VSVQHLQKNYSGTTVFSDINCEIKKGEFVTLLGPSGCGKSTLLRCIAGLTSVDGGKILLE 63

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137
            +D+  +  + R +  VFQSYALFP+MTV +NVAFGLRMQK  A +   RV E L++V+L
Sbjct: 64  GQDLVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVNADDSQKRVAEVLQLVEL 123

Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197
             FA R PHQLSGGQ QRVA+AR++V +PRLLLLDE LSALD ++RK ++ +++ +QR+L
Sbjct: 124 NDFAARYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRQIQREL 183

Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257
           G+T +FVTHDQEEALTMSDRI +M  G+I Q G    +Y  P ++F AGFIG  N+ +A 
Sbjct: 184 GLTTIFVTHDQEEALTMSDRIFLMNQGKIVQSGDAETLYTAPVDVFAAGFIGNYNLLDAD 243

Query: 258 VIERLDEQRV--RANVEGRECNIYVNFAVEPGQKLHVLL 294
              +L ++ +  R  +      + +N  ++   + H LL
Sbjct: 244 SASKLLQRPITHRLAIRPEAIELSLNGELDAQIRSHSLL 282


Lambda     K      H
   0.319    0.136    0.385 

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: 281
Number of extensions: 10
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: 378
Length of database: 329
Length adjustment: 29
Effective length of query: 349
Effective length of database: 300
Effective search space:   104700
Effective search space used:   104700
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 (21.7 bits)
S2: 49 (23.5 bits)

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

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:

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