GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas putida KT2440

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Putida:PP_2753
          Length = 257

 Score =  183 bits (465), Expect = 3e-51
 Identities = 103/245 (42%), Positives = 153/245 (62%), Gaps = 10/245 (4%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHT---- 66
           LL VE++   Y   +  + GV+ RV  G++V ++G NGAGKST  K I GL+        
Sbjct: 14  LLAVEDIEVIYDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAHVS 73

Query: 67  -GKITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLK-- 123
            G I F+G++ AG+ +N + R G+ +V +  +VF  L++EENL  G F+RN + + L+  
Sbjct: 74  RGHIRFQGQDTAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLEQD 133

Query: 124 -DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQV 182
            ++I+A FPRL  +R+ +AG  SGGE+QMLA+G+ALM +P L++LDEPS  L+PI+V ++
Sbjct: 134 LERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVEEI 193

Query: 183 FEQVKQIN-QEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYL 241
           F  V Q+N Q+G + ++ EQN   AL  A   Y+LE+GR    G   EL     +   YL
Sbjct: 194 FAIVAQLNAQQGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHFYL 253

Query: 242 GAGKG 246
           G GKG
Sbjct: 254 G-GKG 257


Lambda     K      H
   0.317    0.136    0.377 

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: 180
Number of extensions: 8
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: 247
Length of database: 257
Length adjustment: 24
Effective length of query: 223
Effective length of database: 233
Effective search space:    51959
Effective search space used:    51959
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: 41 (21.6 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