GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas fluorescens FW300-N1B4

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Pf1N1B4_5611 L-carnitine dehydratase/bile acid-inducible protein F (EC 2.8.3.16)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5611
          Length = 400

 Score =  222 bits (565), Expect = 2e-62
 Identities = 153/407 (37%), Positives = 219/407 (53%), Gaps = 20/407 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  + V+ L   +A P+  + LADLGA VIKVERPG GD  R +      D R      A
Sbjct: 10  LDGITVISLEHAIAAPFCTRQLADLGARVIKVERPGTGDFARGY------DQRVNGL--A 61

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           ++++  NR+K+SVT+D  +     ++  L A +D+L++N   G  A  GL +++L    P
Sbjct: 62  SHFVWTNRSKESVTLDLKQDSATEVLDSLLATADVLVQNLAPGAAARMGLSFEALHQRFP 121

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LI C I+G+G  GPY K+  YD +IQ  GG +S+TG P  +E A   K G ++ DI  G
Sbjct: 122 RLIVCDISGYGVGGPYEKKKAYDLLIQSEGGFLSVTGGPGEEEMA---KAGCSIADIAAG 178

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTG-NAPKRLGNAHPNI 242
           +Y+  AIL+AL  R+  G G H+D+++L+  V  + N  M Y   G   P R G AH  I
Sbjct: 179 MYAYTAILSALLLRERTGEGSHLDVSMLESLVEWM-NYPMYYAYDGAPPPPRAGAAHATI 237

Query: 243 VPYQDFPTADGDFI-LTVGNDGQFRKFAE-VAGQPQWADDPRFATNKVRVANRAVLIPLI 300
            PY  FP  DG  + L + N+ +++ F E V   P+ A D RF+ N  RV NR  L  LI
Sbjct: 238 YPYGPFPIGDGTTVMLGLQNEREWQLFCEKVLLAPELAKDERFSANFKRVENRHALRQLI 297

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
            +A           +LE A +    +ND+  V+  PQ+QAR    E+    AG VP +  
Sbjct: 298 VEAFSTLNFDAVFDRLEHAQIANARVNDMQGVWDHPQLQARDRWREV-ETSAGSVPSLLP 356

Query: 361 PIRLSETPVEYR-NAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           P   S +  E R +A P LG+HT +VL R LGL    +   R AG +
Sbjct: 357 P--GSNSAFEPRMDAVPALGQHTEQVL-RELGLGTDRIEQMRAAGAI 400


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: 424
Number of extensions: 25
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: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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