GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Acidovorax sp. GW101-3H11

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ac3H11_198 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_198
          Length = 404

 Score =  224 bits (571), Expect = 4e-63
 Identities = 150/408 (36%), Positives = 212/408 (51%), Gaps = 24/408 (5%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  LRV++ + ++ GP  G +LADLGA+VIKVE P +GD TR      L  A       A
Sbjct: 15  LEGLRVVEFTHMVMGPTCGMVLADLGAEVIKVE-PVDGDRTR-----HLLGAG------A 62

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            ++   NRNK+S+ +D   PEG    R+LAA +D++ +NFK G +  YGLDY +L  INP
Sbjct: 63  GFFPMFNRNKKSIALDLRSPEGLAAARKLAASADVVAQNFKPGVMTKYGLDYAALSQINP 122

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +LIY + TGF   GPY  R   D ++Q +GGL  +TGRP GD    P++ G ++ DI+ G
Sbjct: 123 RLIYVNHTGF-LPGPYEHRTALDEVVQMMGGLAYMTGRP-GD----PLRAGSSVNDIMGG 176

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           ++     +AAL  R   G GQ +D AL +  V  +    M Y  TG     + +   +  
Sbjct: 177 MFGAIGAMAALMQRGITGRGQEVDSALFENNVFLVGQHMMQYAVTGKPAAPMPDRISSWA 236

Query: 244 PYQDFPTAD-GDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302
            Y  F   D G   L   +D Q++ F +  G      D   ATN  RV  R  L+P++R+
Sbjct: 237 VYDVFSVKDGGQIFLAAVSDAQWQTFCDAMGYADLKADTSLATNNDRVRARPTLMPVLRE 296

Query: 303 ATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARG--LAMELPH-LLAGKVPQVA 359
                T  E     E+ G+P  PI    ++F DP +QA G    + LP    AG+  Q+ 
Sbjct: 297 RLAQHTADELAAVFERHGLPFAPIRRPEELFDDPHLQATGGLADITLPDGERAGQTAQIT 356

Query: 360 -SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
             P+RL    ++ R  PP LG+HT E+LQ  LG     V A   AG +
Sbjct: 357 LLPLRLDGQRLDVRCDPPRLGQHTAELLQG-LGYTADEVAALHAAGTI 403


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: 462
Number of extensions: 25
Number of successful extensions: 6
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: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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