GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudomonas putida KT2440

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate PP_1722 PP_1722 ABC transporter, ATP-binding protein

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__Putida:PP_1722
          Length = 329

 Score =  218 bits (555), Expect = 2e-61
 Identities = 122/293 (41%), Positives = 179/293 (61%), Gaps = 18/293 (6%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           M+ V+ +    SY G+  P  ++ +  I  GEF+ L+GPSGCGKST LR +AGL +V  G
Sbjct: 1   MSFVSVQKLQKSYAGS--PVFERIDCHIERGEFVTLLGPSGCGKSTLLRCIAGLTSVDSG 58

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            I +   D+  ++P+ R I MVFQ+YAL+P+MTV +N+ F L++     DE   RV E  
Sbjct: 59  QILLDGHDIVPLSPQKRGIGMVFQSYALFPNMTVEQNVAFGLRMQKVKADESQLRVREVL 118

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             + L +F  R P  LSGGQ QRVA+ R++V  P++ L+DEPLS LDA++R   R QI A
Sbjct: 119 ELVELGKFAGRYPHQLSGGQCQRVALARSLVTRPRLLLLDEPLSALDARIRKHLREQIRA 178

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           +QR+LG+TT++VTHDQ EALTM DRI ++  G + Q G    LY  P ++F AGFIG+  
Sbjct: 179 IQRELGLTTIFVTHDQEEALTMSDRIFLMNQGRIVQSGDAETLYTAPVDLFAAGFIGN-- 236

Query: 241 MNLGTFSVKDGDATSG------HARIKLSPETLAAMTPEDNGRITIGFRPEAL 287
                +++ D D+ S        +R+ + PE++   T  ++G +    R  +L
Sbjct: 237 -----YNLLDADSASRLLQRPVASRLAIRPESI---TLGEHGELDAEVRSHSL 281


Lambda     K      H
   0.316    0.135    0.380 

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: 289
Number of extensions: 13
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: 376
Length of database: 329
Length adjustment: 29
Effective length of query: 347
Effective length of database: 300
Effective search space:   104100
Effective search space used:   104100
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: 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