GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas fluorescens GW456-L13

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate PfGW456L13_1728 L-carnitine dehydratase/bile acid-inducible protein F (EC 2.8.3.16)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1728
          Length = 399

 Score =  221 bits (564), Expect = 2e-62
 Identities = 142/407 (34%), Positives = 218/407 (53%), Gaps = 19/407 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           LS L+V++L  ++AGP+A +I A+ GADVIK+E P  GD  R W   +         T  
Sbjct: 8   LSGLKVIELGTLIAGPFASRICAEFGADVIKIESPDGGDPLRKWRKLY-------EGTSL 60

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            +++ A RNK+S+T++   P+GQ ++++L  ++DILIENF+ G L   GL +D L A+NP
Sbjct: 61  WWFVQA-RNKKSLTLNLKHPDGQAILKQLLGEADILIENFRPGVLEKLGLGWDVLHALNP 119

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +L+   ++GFGQTGP   + G+  + + +GGL  +T    G E   PV+ G+++ D +  
Sbjct: 120 KLVMVRLSGFGQTGPMKDQPGFGAVGESMGGLRYIT----GFEDRPPVRTGISIGDSIAA 175

Query: 184 LYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242
           L+     L AL HR+  GG GQ +D+AL +   A + +    +   G   +R GN  P I
Sbjct: 176 LWGVIGALMALRHREVNGGLGQVVDVALYEAIFAMMESMVPEFDVFGFIRERTGNIMPGI 235

Query: 243 VPYQDFPTADGDFI-LTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
            P     +ADG  + +    D  F++F  + G+   A+DP+ A+N  R A R  +  +I 
Sbjct: 236 TPSSIHTSADGKHVQIGANGDAIFKRFMLIIGREDLANDPQLASNDGRDARRDEIYGVID 295

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAME--LPHLLAGKVPQVA 359
           +          + QL QA VP   I     +F DPQ  AR + ++  LP     K+P + 
Sbjct: 296 RWVNSLPLDRVLAQLNQAEVPASRIFSAEDMFNDPQYLAREMFLQAKLPDGKDFKMPGIV 355

Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
              +LSETP E     P LGEH  +VLQ  LG D   +   R+ G +
Sbjct: 356 P--KLSETPGECEWVGPQLGEHNAQVLQE-LGYDATQIAQLRKDGAI 399


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: 455
Number of extensions: 23
Number of successful extensions: 7
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: 399
Length adjustment: 31
Effective length of query: 375
Effective length of database: 368
Effective search space:   138000
Effective search space used:   138000
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