GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloB in Herbaspirillum seropedicae SmR1

Align palmitoyl-CoA hydrolase (EC 3.1.2.2) (characterized)
to candidate HSERO_RS13610 HSERO_RS13610 S-formylglutathione hydrolase

Query= BRENDA::P33018
         (278 letters)



>FitnessBrowser__HerbieS:HSERO_RS13610
          Length = 282

 Score =  276 bits (706), Expect = 4e-79
 Identities = 143/275 (52%), Positives = 179/275 (65%), Gaps = 3/275 (1%)

Query: 1   MEMLEEHRCFEGWQQRWRHDSSTLNCPMTFSIFLPPPRDH-TPPPVLYWLSGLTCNDENF 59
           +E L EH CF G Q  +RH S  +   M FS+F+PP     +P PVL++L+GLTC +E F
Sbjct: 2   LETLSEHGCFGGVQGYYRHASPAIGLDMRFSVFVPPQASKGSPLPVLFYLAGLTCTEETF 61

Query: 60  TTKAGAQRVAAELGIVLVMPDTSPRGEKVAND-DGYDLGQGAGFYLNATQPPWATHYRMY 118
             KAGAQRVAAELG++LV  DTSPRG  +A + D +D G GAGFYL+ATQ PW+ HYRM 
Sbjct: 62  MIKAGAQRVAAELGMILVASDTSPRGAGIAGESDSWDFGVGAGFYLDATQAPWSQHYRME 121

Query: 119 DYLRDELPALVQSQFNVS-DRCAISGHSMGGHGALIMALKNPGKYTSVSAFAPIVNPCSV 177
            Y+ D+L   V   F     R  + GHSMGGHGAL +AL++   Y SVSAFAPI  P + 
Sbjct: 122 SYVVDDLRRAVLDNFPADPQRMGVFGHSMGGHGALTLALRHRDVYRSVSAFAPIAAPINC 181

Query: 178 PWGIKAFSSYLGEDKNAWLEWDSCALMYASNAQDAIPTLIDQGDNDQFLADQLQPAVLAE 237
            WG KAFS YLG D+ AW + D+  LM A         LIDQG  D+FLA+QL P     
Sbjct: 182 AWGQKAFSHYLGTDRQAWKQHDASELMRALQTPFPQGILIDQGLADKFLAEQLLPERFEA 241

Query: 238 AARQKAWPMTLRIQPGYDHSYYFIASFIEDHLRFH 272
           A ++ + P++LR   GYDH YYFI +F+EDHLRFH
Sbjct: 242 ACKEASQPLSLRRHAGYDHGYYFIETFMEDHLRFH 276


Lambda     K      H
   0.320    0.136    0.441 

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: 290
Number of extensions: 8
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: 278
Length of database: 282
Length adjustment: 26
Effective length of query: 252
Effective length of database: 256
Effective search space:    64512
Effective search space used:    64512
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 (21.8 bits)
S2: 47 (22.7 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