GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF1363
          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.

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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