GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Pseudomonas putida KT2440

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate PP_0220 PP_0220 methionine import ATP-binding protein metN2

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Putida:PP_0220
          Length = 369

 Score =  270 bits (691), Expect = 3e-77
 Identities = 155/316 (49%), Positives = 208/316 (65%), Gaps = 12/316 (3%)

Query: 2   IEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGR 61
           + F  + KTY   G+  PALQ   LNI+ G+IFG+IG SGAGKS+LLR INRLE+PS GR
Sbjct: 33  VRFIGLGKTY--PGQAQPALQGIDLNIRHGEIFGIIGRSGAGKSSLLRTINRLEQPSQGR 90

Query: 62  ILVEGEDVTALDAEGLRRFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDAR 121
           +L++  D+   + + L   R+R+GMIFQHFNL+S+KTV  N+ +PL++AG  ++AE   +
Sbjct: 91  VLIDQVDIAPFNEDQLVALRRRIGMIFQHFNLMSAKTVWQNVELPLKVAG-VAKAERQRK 149

Query: 122 VSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVL 181
           V ELL  VGL +    YPAQLSGGQKQRVGIARAL   P ILLCDEATSALDP+TTAS+L
Sbjct: 150 VRELLELVGLQEKHHVYPAQLSGGQKQRVGIARALVHTPEILLCDEATSALDPETTASIL 209

Query: 182 QLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRF 241
           +LL +IN+ L LTIVLITHEM VIR +C +V V++ GA+VEQG+V  VF  P+H  TR  
Sbjct: 210 ELLRDINQRLGLTIVLITHEMAVIRDICHRVVVLERGAVVEQGEVWRVFGSPRHEVTRTL 269

Query: 242 VFEAE-----RVDEDERHDDFAHVPGLILRLTFRGEATYAPLLGTVARQTGVDYSILSGR 296
           +   +      +    +    +    ++L+LT  GE    P L  +    G    +L G 
Sbjct: 270 LAPLQAKLPAALQASLQAHPASGNSAVVLKLTVLGE----PELSALFNDLGGRVRLLQGG 325

Query: 297 IDRIKDTPYGQLTLAL 312
           ++ I +   GQL L++
Sbjct: 326 VETIGEHALGQLILSV 341


Lambda     K      H
   0.322    0.138    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: 362
Number of extensions: 10
Number of successful extensions: 2
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: 335
Length of database: 369
Length adjustment: 29
Effective length of query: 306
Effective length of database: 340
Effective search space:   104040
Effective search space used:   104040
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 (21.9 bits)
S2: 49 (23.5 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