GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Herbaspirillum seropedicae SmR1

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate HSERO_RS19995 HSERO_RS19995 3-oxoadipate CoA-transferase subunit B

Query= reanno::psRCH2:GFF1044
         (209 letters)



>FitnessBrowser__HerbieS:HSERO_RS19995
          Length = 213

 Score =  239 bits (611), Expect = 2e-68
 Identities = 116/207 (56%), Positives = 154/207 (74%), Gaps = 1/207 (0%)

Query: 3   WTREQMAQRAAQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEI 62
           +TRE++A R AQ++ +G YVNLGIGLPT VANY+P   +++L SENG+LG+GP P   E 
Sbjct: 4   FTREEIAARVAQDIPEGAYVNLGIGLPTKVANYLPADKEIFLHSENGVLGMGPAPAPGEE 63

Query: 63  DPDLINAGKQTVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMIPG-K 121
           D DLINAGKQ VT L G ++F +A SFAM+RGGH+++ +LGA QVS KGDLANW      
Sbjct: 64  DEDLINAGKQPVTLLTGGAYFHHADSFAMMRGGHLDICVLGAFQVSAKGDLANWHTGAPD 123

Query: 122 MVKGMGGAMDLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVT 181
            +  +GGAMDL  G K+V V+M+H  K G  K++ AC  PLTG+G V+RI TDL V+DVT
Sbjct: 124 AIPAVGGAMDLAIGAKQVFVMMDHQTKTGESKLVEACSYPLTGIGCVNRIYTDLAVIDVT 183

Query: 182 EQGLKLVELAEGVSFDELQEATGSPIQ 208
             GL++ E+ EG+SFDELQ+ TG+P++
Sbjct: 184 PHGLQVREIVEGLSFDELQKLTGAPLR 210


Lambda     K      H
   0.318    0.138    0.404 

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: 192
Number of extensions: 6
Number of successful extensions: 2
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: 209
Length of database: 213
Length adjustment: 21
Effective length of query: 188
Effective length of database: 192
Effective search space:    36096
Effective search space used:    36096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 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