GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Pseudomonas putida KT2440

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PP_2753 PP_2753 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Putida:PP_2753
          Length = 257

 Score =  175 bits (443), Expect = 9e-49
 Identities = 99/243 (40%), Positives = 147/243 (60%), Gaps = 9/243 (3%)

Query: 2   SDLLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP---- 57
           S+LL V+D+   Y   +  + G++  +  G++V ++G NGAGKST  K I GL+      
Sbjct: 12  SELLAVEDIEVIYDGTILAVAGVSLRVGQGDIVALLGANGAGKSTTLKAISGLVQADRAH 71

Query: 58  -SQGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLK 116
            S+G I F+G++  G+ ++ + R+G+ +V +  +VF  LT+ ENL  G FL     + L+
Sbjct: 72  VSRGHIRFQGQDTAGVAANLLARQGIVHVLEGRHVFSHLTIEENLRSGGFLRNPTRRQLE 131

Query: 117 ---DRIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVK 173
              +RIY  FP+L  +R  +AG  SGGE+QMLA+GRALM  P L+LLDEPS  L+PI+V+
Sbjct: 132 QDLERIYAWFPRLKTKRKTQAGLTSGGEQQMLAIGRALMTKPRLVLLDEPSMGLAPIIVE 191

Query: 174 DVFAQIKAINA-TGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGEL 232
           ++FA +  +NA  G + ++ EQN   AL  A   Y+LENGR   EGS   L     +   
Sbjct: 192 EIFAIVAQLNAQQGVSFLVAEQNINVALRYASHAYILENGRVVGEGSAAELAAREDIQHF 251

Query: 233 YLG 235
           YLG
Sbjct: 252 YLG 254


Lambda     K      H
   0.320    0.139    0.393 

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: 152
Number of extensions: 7
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: 240
Length of database: 257
Length adjustment: 24
Effective length of query: 216
Effective length of database: 233
Effective search space:    50328
Effective search space used:    50328
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