GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaF in Herbaspirillum seropedicae SmR1

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate HSERO_RS19405 HSERO_RS19405 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19405 HSERO_RS19405 enoyl-CoA
           hydratase
          Length = 258

 Score =  383 bits (984), Expect = e-111
 Identities = 191/257 (74%), Positives = 219/257 (85%)

Query: 1   MAYENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA 60
           M+YENI VET  +VGL+ L+RPKALNAL+D LM ELG AL  FDA + IG I++TGSEKA
Sbjct: 1   MSYENIQVETHEKVGLIRLHRPKALNALSDGLMTELGEALLAFDAQEEIGCIIITGSEKA 60

Query: 61  FAAGADIGMMSTYTYMDVYKGDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDII 120
           FAAGADI  M+ Y YMDV+KG++ITRNWET+R IRKP+IAAVAG+ALGGGCELAMMCD I
Sbjct: 61  FAAGADISAMAGYDYMDVFKGEFITRNWETLRRIRKPVIAAVAGYALGGGCELAMMCDFI 120

Query: 121 FAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180
            AAD AKFGQPEIKLGI+PGAGGTQRLPRAVSKAKAMDL LT R MDA EAERAGLVSR+
Sbjct: 121 IAADNAKFGQPEIKLGIVPGAGGTQRLPRAVSKAKAMDLALTGRMMDAEEAERAGLVSRI 180

Query: 181 IPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQ 240
           + A  L++EA+AAA  IAE P    MMVK+SVNRAYETTL+EG+ +ER LF+S FATEDQ
Sbjct: 181 VAADKLLEEAMAAAIIIAEMPRQVAMMVKDSVNRAYETTLSEGMKYERALFYSCFATEDQ 240

Query: 241 KEGMAAFVEKRKPVFKH 257
           KEGM AF+EKR+PVFKH
Sbjct: 241 KEGMKAFLEKRQPVFKH 257


Lambda     K      H
   0.321    0.134    0.380 

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: 258
Number of extensions: 3
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: 258
Length of database: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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 (21.9 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