GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas putida KT2440

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate PP_3001 PP_3001 CAIB/BAIF family protein

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Putida:PP_3001
          Length = 410

 Score =  233 bits (593), Expect = 1e-65
 Identities = 141/409 (34%), Positives = 212/409 (51%), Gaps = 18/409 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L+ +RV+D S  LAGP+ G+ LA LGA+VIKVERPG+GD  R       + A   +  ++
Sbjct: 7   LAGIRVVDYSHFLAGPYVGRCLAALGAEVIKVERPGSGDAGR-------QHAFTLDDQQS 59

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            Y+L  N  KQ V+++   P G+  ++ L   +D+ IEN++ G L   GL Y  L A NP
Sbjct: 60  GYFLQLNMGKQGVSVNMKDPRGKAFMQRLTDSADVFIENYRPGALDKLGLGYAELSARNP 119

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +L+YCSI+ +G TGP A RAG+  + +   G+M + G P    G  P  + ++L D+ TG
Sbjct: 120 RLVYCSISAYGHTGPDAHRAGFGLIAEAKSGIMQMVGVP----GEAPPLLRISLGDMYTG 175

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNA--PKRLGNAHPN 241
           +++ AAI AAL  R   G GQHIDMAL D  V+        Y  +G    P++ G+  P 
Sbjct: 176 IHAVAAINAALLGRVSSGRGQHIDMALYDTLVSMHEYAVQCYTLSGGTVLPQQTGHDMPT 235

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEV----AGQPQWADDPRFATNKVRVANRAVLI 297
              Y  F   DGD ++    D  +++FA +     G P +  D R+     R A+R  ++
Sbjct: 236 STLYGVFRATDGDLVIAAQVDDAWQRFAAMLEANGGPPGFGSDRRYHGLNGRNAHREAIL 295

Query: 298 PLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQ 357
            ++R     +  AE +  L+   +P   +  + +V ADPQ+QAR + +E  H   G +  
Sbjct: 296 AVVRDWVGARRVAEILALLDGIDIPSAKVQRIDEVLADPQIQARNMVIEQQHPRYGTLRL 355

Query: 358 VASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
              P R S+         P LG+H  EV    LG     + A +  GVL
Sbjct: 356 ANLPFRFSDCDTTIHQVAPDLGQHNAEVAAG-LGFSPEEITALQADGVL 403


Lambda     K      H
   0.319    0.137    0.408 

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: 437
Number of extensions: 19
Number of successful extensions: 5
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: 406
Length of database: 410
Length adjustment: 31
Effective length of query: 375
Effective length of database: 379
Effective search space:   142125
Effective search space used:   142125
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 (21.7 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:

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