GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malK_Aa in Pseudomonas putida KT2440

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>lcl|FitnessBrowser__Putida:PP_0411 PP_0411 Polyamine ABC
           transporter, ATP-binding protein
          Length = 374

 Score =  251 bits (642), Expect = 2e-71
 Identities = 140/286 (48%), Positives = 182/286 (63%), Gaps = 13/286 (4%)

Query: 9   IYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRR 68
           + K+Y G++   VKD NLDI+  EF   +GPSG GKTT+L M+AG E  T G + +G R 
Sbjct: 20  VQKSYDGESL-IVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGRS 78

Query: 69  VNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHL 128
           +N+VPP  RDI MVFQNYAL+PHMTV +N+AF L +R + K +I  RV+    ++ +   
Sbjct: 79  INNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDAF 138

Query: 129 LDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTT 188
             R P  LSGGQ+QRVAL RA+V EPQ+ LMDEPL  LD +LR  M+ EI+ +HQRL  T
Sbjct: 139 AKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLGVT 198

Query: 189 VIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEI 248
           V+YVTHDQ EA+TM DR+ V   G IQQ   P+ +Y +P N FVA FIG    N I G +
Sbjct: 199 VVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGE--NNRISGTL 256

Query: 249 V-QDGDAFYFRAPSISLRLPEG-RYGVLKAS-GAIGKPVVLGVRPE 291
           +  DG           ++LP G R   L  + G  G+PV L +RPE
Sbjct: 257 LASDG-------KRCQVQLPRGERVEALAVNVGQAGEPVTLSIRPE 295


Lambda     K      H
   0.321    0.138    0.395 

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: 350
Number of extensions: 15
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: 384
Length of database: 374
Length adjustment: 30
Effective length of query: 354
Effective length of database: 344
Effective search space:   121776
Effective search space used:   121776
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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