GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Pseudomonas putida KT2440

Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate PP_0227 PP_0227 periplasmic cystine-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09900
         (251 letters)



>FitnessBrowser__Putida:PP_0227
          Length = 264

 Score =  138 bits (348), Expect = 1e-37
 Identities = 84/263 (31%), Positives = 150/263 (57%), Gaps = 22/263 (8%)

Query: 1   MQTYKKFLLAAAVSLVFSAN----AMAADKLK---------MGIEAAYPPFNNKDASGQV 47
           M  + K LL A+++L+  A     A A ++LK         +G+E  YPPF+ +D +G++
Sbjct: 1   MSKFAKPLLNASLALLLGAGLLSQAFAGEQLKTIQEKGVINVGLEGTYPPFSFQDENGKL 60

Query: 48  VGFDKDIGDALCAKMKVECEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDP 107
            GF+ ++ + L  ++ V+ ++  + WDGI+ AL +K+ D +++ ++I+EERK+  DF++P
Sbjct: 61  TGFEVELSELLAKELGVKAKIQPTKWDGILAALESKRLDVVVNQVTISEERKKKYDFSEP 120

Query: 108 YYSNKLQ-FIAPKSAEFKTDK--DSLKGKVIGAQRATLAGTWLEDEL-GSDITTKLYDTQ 163
           Y  + +Q  I  K AE    K    L GK +G    T    W++ ++  +D+ T  Y+  
Sbjct: 121 YTVSGIQALILKKKAEQLNIKGAQDLAGKKVGVGLGTNYEQWVKKDVPQADVRT--YEDD 178

Query: 164 ENAYLDLTSGRVDAILADKYVNYDWLKTEAGRAYEFKGDPVVESDKIGIAVRKGDNELRN 223
            + + DL +GR+DAIL D+    ++   +  +  E  GD     +  G+A+RKG+ EL  
Sbjct: 179 PSKFADLRNGRIDAILIDRLAALEY--AQKAKDTELAGDAFSRLES-GVALRKGEPELLA 235

Query: 224 KLNAALKEIVADGTYKKINDKYF 246
            +N A+ ++ ADGT  K+++KYF
Sbjct: 236 AINKAIDKLKADGTLAKLSEKYF 258


Lambda     K      H
   0.316    0.133    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: 164
Number of extensions: 8
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: 251
Length of database: 264
Length adjustment: 24
Effective length of query: 227
Effective length of database: 240
Effective search space:    54480
Effective search space used:    54480
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: 47 (22.7 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