GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Sphingomonas koreensis DSMZ 15582

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ga0059261_2807 Ga0059261_2807 Predicted acyl-CoA transferases/carnitine dehydratase

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



>FitnessBrowser__Korea:Ga0059261_2807
          Length = 403

 Score =  384 bits (987), Expect = e-111
 Identities = 202/404 (50%), Positives = 262/404 (64%), Gaps = 13/404 (3%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L+  RVLDLSRVLAGPW   +LADLGA+V KVE P  GDDTR WGPP+          E+
Sbjct: 11  LAGRRVLDLSRVLAGPWCTMVLADLGAEVTKVEHPRGGDDTRHWGPPYTGG-------ES 63

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           AYYL ANRNK+SV +D ++PEGQR+VR+LAA++D+L+EN+K+GGL  +GLDY S+ AINP
Sbjct: 64  AYYLCANRNKRSVALDISKPEGQRIVRDLAAQADVLVENYKLGGLEKFGLDYSSIAAINP 123

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +++YCSI+G+G+  P A+R GYD++IQ  GGLMS+TG  +G+    P+KVGVA+ D+ TG
Sbjct: 124 RIVYCSISGYGRRSPIAERPGYDYVIQAEGGLMSVTGPVDGE----PMKVGVAVADLFTG 179

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           + +  AILAAL   D  G GQH+DMAL D Q+A LAN     L  G  P+R GN HP +V
Sbjct: 180 MAAAQAILAALIAADRDGAGQHLDMALYDCQLAMLANVGSAALVAGTEPRRYGNGHPTVV 239

Query: 244 PYQDFPTADGDFILTVGNDGQFRKFA-EVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302
           PYQ F T DG  ++ VGND QF  FA  +  +P  A D RFA N  RVANR  L+  I  
Sbjct: 240 PYQLFDTLDGQVVVAVGNDAQFTAFATRLLDRPDLATDERFAKNGSRVANRDALLAEIMP 299

Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPI 362
                TT  W+  L   GVP G +  + +  A P+  AR +   + H  AG+V  VASP+
Sbjct: 300 LMRRHTTEWWLAGLRSVGVPTGAVRQVGEALAAPEATARDMVATVAHPSAGEVKLVASPL 359

Query: 363 RLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           +L  TPV    APP+LG+H+  VL   LG     + A  E GV+
Sbjct: 360 KLGRTPVVSPVAPPMLGQHSRTVLAE-LGYRADEIEALFETGVI 402


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: 523
Number of extensions: 17
Number of successful extensions: 4
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: 403
Length adjustment: 31
Effective length of query: 375
Effective length of database: 372
Effective search space:   139500
Effective search space used:   139500
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 (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