GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1701 ABC transporter ATP-binding protein

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1701
          Length = 258

 Score =  197 bits (500), Expect = 2e-55
 Identities = 111/242 (45%), Positives = 156/242 (64%), Gaps = 9/242 (3%)

Query: 1   MLQFENVSTFY-GKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHS---- 55
           +L  +++   Y G I A+  V++ V QG+IV L+GANGAGKST L  + G  QA      
Sbjct: 14  LLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQVS 73

Query: 56  -GSIRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTD--KGDYQEQ 112
            G I + G +  G  ++ + R+ I  V EGR VFA LTVE+NL  GGF     +   ++ 
Sbjct: 74  RGRIVFQGRDTAGVAANLLARQGIVHVLEGRHVFAHLTVEDNLRSGGFLRKPTRRALEQD 133

Query: 113 MDKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQI 172
           ++++   FPRLK +   + G  SGGEQQMLAIGRALM+KP+L+LLDEPS+GLAP+++++I
Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPLLVEEI 193

Query: 173 FDIIEQLR-KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYL 231
           F I+ QL  ++GV+  + EQN N AL+ A  AY+LENGRVV +G   AL     ++  YL
Sbjct: 194 FAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATALAAREDIQHFYL 253

Query: 232 GG 233
           GG
Sbjct: 254 GG 255


Lambda     K      H
   0.320    0.137    0.381 

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: 184
Number of extensions: 9
Number of successful extensions: 4
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: 233
Length of database: 258
Length adjustment: 24
Effective length of query: 209
Effective length of database: 234
Effective search space:    48906
Effective search space used:    48906
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: 46 (22.3 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