GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Herbaspirillum seropedicae SmR1

Align 2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase

Query= metacyc::MONOMER-15953
         (257 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS20665 HSERO_RS20665
           2,3-dehydroadipyl-CoA hydratase
          Length = 262

 Score =  269 bits (688), Expect = 4e-77
 Identities = 139/241 (57%), Positives = 176/241 (73%)

Query: 17  ITLQRPEALNALNTQLLDELAAELALAEQDAETRAVVLTGSRKAFAAGADIKEMAERDLV 76
           +TL RP   NAL  Q L E+ A LA AE+D   R VV++G+ KAFAAGAD+ EM  +D +
Sbjct: 22  LTLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISGNEKAFAAGADLNEMIHKDAI 81

Query: 77  GILEDPRVAHWQRIAAFSKPLIAAVNGFCLGGGCELAMHADILIAGEDARFGQPEINLGI 136
               D R  +W+ IA F KP++AAVNG+ LG GCEL MHADI IA   A+ GQPEIN+G 
Sbjct: 82  ATQLDVRAQYWRAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKIGQPEINVGT 141

Query: 137 MPGAGGTQRLLRAVGKSLAMQMVLSGQAIDARHAQRAGLVSEVTLPELTIERALAIARVI 196
           +PGAGGTQRL+R VGK LAM+MVLSG+ I A  A +AGLV+EV   + T+ER LA+A  I
Sbjct: 142 LPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLERTLALAHSI 201

Query: 197 AQKAPLAVRLAKEALLKAEDTDLASGLRFERHAFTVLAGTADRAEGIRAFQEKRRPEFTG 256
           AQK+PLAVRLAKEA+L++ +  L +GL FER +F+++A +ADR EGI AFQEKR   F+G
Sbjct: 202 AQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQEKRAAVFSG 261

Query: 257 R 257
           R
Sbjct: 262 R 262


Lambda     K      H
   0.320    0.134    0.374 

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: 200
Number of extensions: 9
Number of successful extensions: 1
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: 257
Length of database: 262
Length adjustment: 24
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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