GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Pseudomonas putida KT2440

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Putida:PP_1722
          Length = 329

 Score =  229 bits (584), Expect = 8e-65
 Identities = 115/236 (48%), Positives = 156/236 (66%)

Query: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60
           MS + +  ++KSY G  V + +D  I+ GEFV  +GPSGCGKSTLLR IAGL  + SG +
Sbjct: 1   MSFVSVQKLQKSYAGSPVFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSGQI 60

Query: 61  TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120
            +D   +  + P KRGI MVFQSYAL+P+MTV +N+ F LR   V   E + RV E   +
Sbjct: 61  LLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVLEL 120

Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180
           +ELG    R P QLSGGQ QRVA+ R++V  P++ L DEPLS LDA +R H+R +I  + 
Sbjct: 121 VELGKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRAIQ 180

Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGS 236
           ++L  T ++VTHDQ EA+T++D+I +M  G + Q G    LY  P +LF AGFIG+
Sbjct: 181 RELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIGN 236


Lambda     K      H
   0.321    0.139    0.396 

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: 302
Number of extensions: 10
Number of successful extensions: 1
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: 358
Length of database: 329
Length adjustment: 29
Effective length of query: 329
Effective length of database: 300
Effective search space:    98700
Effective search space used:    98700
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: 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