GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Pf6N2E2_1701 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1701
          Length = 258

 Score =  200 bits (508), Expect = 3e-56
 Identities = 110/242 (45%), Positives = 160/242 (66%), Gaps = 8/242 (3%)

Query: 3   VLKVENLSVHY-GMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRP-----S 56
           +L V+++ V Y G I AV  VS  V +G++V+L+GANGAGK+T L+ +SGLV+      S
Sbjct: 14  LLAVQDIEVIYDGAILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAQVS 73

Query: 57  SGKIEFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK-NREENQAN 115
            G+I F G++   + A  +   G+  V EGRHVF  LTV +NL  G FL+K  R   + +
Sbjct: 74  RGRIVFQGRDTAGVAANLLARQGIVHVLEGRHVFAHLTVEDNLRSGGFLRKPTRRALEQD 133

Query: 116 LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEI 175
           L+++++ FPRL+ ++   A   SGGEQQMLA+GRALM+ P+L+LLDEPSMGLAP+ ++EI
Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPLLVEEI 193

Query: 176 FDIIQDIQKQ-GTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYL 234
           F I+  +  Q G + L+ EQN N AL  +   Y+LE G++V  G    LA+ E+++  YL
Sbjct: 194 FAIVAQLNAQEGVSFLVAEQNINVALRHASYAYILENGRVVGEGDATALAAREDIQHFYL 253

Query: 235 GG 236
           GG
Sbjct: 254 GG 255


Lambda     K      H
   0.315    0.134    0.358 

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: 176
Number of extensions: 12
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: 236
Length of database: 258
Length adjustment: 24
Effective length of query: 212
Effective length of database: 234
Effective search space:    49608
Effective search space used:    49608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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