GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Pseudomonas fluorescens FW300-N2E2

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Pf6N2E2_1705 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:D8J1T6
         (255 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1705 Branched-chain amino
           acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
          Length = 256

 Score =  199 bits (507), Expect = 4e-56
 Identities = 101/252 (40%), Positives = 157/252 (62%), Gaps = 1/252 (0%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL++R+VS  F G++A++ +  +++ G+I  LIGPNGAGK++  N++ G+Y+ D G    
Sbjct: 4   LLEVRNVSLSFRGVKAISDLSFSVKLGEICALIGPNGAGKSSLLNILNGVYRADAGQLFF 63

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
             +P     P + A+ GI RTFQN  LF +M+V++N++ G     +            AR
Sbjct: 64  AAEPLHRPHPLKAARLGIGRTFQNNALFKKMSVVDNLLTGLSRFQRTFFLEQALGLPRAR 123

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
            E  A  E+++++L+F+ +  +       L+YG Q+R+E+ RAL   P LL LDEP AGM
Sbjct: 124 REARAFAERAERVLEFLELQAWRDVAVGSLAYGLQKRVELGRALIAQPTLLLLDEPMAGM 183

Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243
           NA EK  +   +  I  + G T++LIEHD++++MGL + + VLDYG+ + +G PA+VQ N
Sbjct: 184 NAEEKQDMSRFITDINRDLGTTVILIEHDIQVVMGLSSHVVVLDYGRKVGDGSPAEVQVN 243

Query: 244 PAVIEAYLGAGH 255
           P VI AYLGA H
Sbjct: 244 PEVIAAYLGASH 255


Lambda     K      H
   0.320    0.138    0.394 

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: 166
Number of extensions: 7
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: 255
Length of database: 256
Length adjustment: 24
Effective length of query: 231
Effective length of database: 232
Effective search space:    53592
Effective search space used:    53592
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.

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 preprint 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