GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Pseudomonas fluorescens FW300-N2E2

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Pf6N2E2_1705 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1705
          Length = 256

 Score =  182 bits (463), Expect = 5e-51
 Identities = 108/260 (41%), Positives = 155/260 (59%), Gaps = 13/260 (5%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL V ++++ F G+ A++D+SFS   GEI A+IGPNGAGK++L N + G Y    G+L  
Sbjct: 4   LLEVRNVSLSFRGVKAISDLSFSVKLGEICALIGPNGAGKSSLLNILNGVYRADAGQLF- 62

Query: 71  RHADGKEFLLERM--PGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128
                  F  E +  P    + +  + RTFQN  LF  MSV++NL+    ++  R   F 
Sbjct: 63  -------FAAEPLHRPHPLKAARLGIGRTFQNNALFKKMSVVDNLLTGL-SRFQRT--FF 112

Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPV 188
           +   LGLP   R  R   + A+  L+ + L  + D   G+L YG Q+R+E+ RA+  +P 
Sbjct: 113 LEQALGLPRARREARAFAERAERVLEFLELQAWRDVAVGSLAYGLQKRVELGRALIAQPT 172

Query: 189 MLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKI 248
           +L LDEP AG+N  E  +++  +T I  +    V+LIEHD+ VVM +S HVVVLDYGRK+
Sbjct: 173 LLLLDEPMAGMNAEEKQDMSRFITDINRDLGTTVILIEHDIQVVMGLSSHVVVLDYGRKV 232

Query: 249 SDGDPAFVKNDPAVIRAYLG 268
            DG PA V+ +P VI AYLG
Sbjct: 233 GDGSPAEVQVNPEVIAAYLG 252


Lambda     K      H
   0.319    0.137    0.397 

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: 179
Number of extensions: 5
Number of successful extensions: 3
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: 294
Length of database: 256
Length adjustment: 25
Effective length of query: 269
Effective length of database: 231
Effective search space:    62139
Effective search space used:    62139
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: 47 (22.7 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