GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdG in Pseudomonas simiae WCS417

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF1363 PS417_06930 carnitine dehydratase

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



>lcl|FitnessBrowser__WCS417:GFF1363 PS417_06930 carnitine
           dehydratase
          Length = 397

 Score =  221 bits (564), Expect = 2e-62
 Identities = 138/407 (33%), Positives = 221/407 (54%), Gaps = 19/407 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           LS ++V+++  ++A P+A +++A+ GA+VIK+E  G GD  R W        +    T  
Sbjct: 5   LSGIKVVEIGTLIAAPFAARMMAEFGAEVIKIEAMGQGDPLRKW-------RKLHEGTSL 57

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            +YL + RNK+S+ +D   PEG  L+++L   +D+LIEN + GGL   GL +D L A+NP
Sbjct: 58  WWYLQS-RNKKSLALDLKSPEGLDLIKQLLGDADVLIENLRPGGLEKLGLGWDVLHALNP 116

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +L    I+G+GQTGPY  R G+  + + +GG+   TG P+    + P +VGV+L D L  
Sbjct: 117 KLTLVRISGYGQTGPYRDRPGFGAIGEAMGGIRYTTGNPD----SPPARVGVSLGDSLAS 172

Query: 184 LYST-AAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242
           L+    A+++ L  +   G GQ +D++L +     + +    Y   G+  +R G A P I
Sbjct: 173 LHGVIGALMSLLRVKTGQGDGQIVDVSLAESVFNLMESLVPEYDMLGHVRERSGGALPGI 232

Query: 243 VPYQDFPTADGDFILTVGN-DGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
            P   + TADG +++  GN D  +++     G+   A+ P F  N  R A   +L   I 
Sbjct: 233 APSNTYLTADGAYVVIAGNSDPIYKRLMTTIGRADLAEAPEFVHNDGRAAKSGLLDAAIT 292

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAM--ELPHLLAGKVPQVA 359
             T  +   + ++ LE A VP G I  +A + +DP  QAR + +  ELP  ++ K+P + 
Sbjct: 293 HWTSSRPIEQVLSALEAAEVPAGRIYSVADIVSDPHYQARDMLLNAELPGGVSVKMPGIV 352

Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
              +LSETP       P LG+HT ++L   LGL  A +   + AGV+
Sbjct: 353 P--KLSETPGGVNWQGPTLGQHTDDILGS-LGLTGADIQRLKTAGVV 396


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: 467
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: 397
Length adjustment: 31
Effective length of query: 375
Effective length of database: 366
Effective search space:   137250
Effective search space used:   137250
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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