GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Pseudomonas fluorescens FW300-N2C3

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate AO356_01585 AO356_01585 methylcrotonoyl-CoA carboxylase

Query= reanno::pseudo5_N2C3_1:AO356_01585
         (535 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01585 AO356_01585
           methylcrotonoyl-CoA carboxylase
          Length = 535

 Score = 1070 bits (2768), Expect = 0.0
 Identities = 535/535 (100%), Positives = 535/535 (100%)

Query: 1   MATLHTQLNPRSPEFIANREAMLGHVEALRTLLAQIRQGGGLKAQERHTSRGKLLPRERI 60
           MATLHTQLNPRSPEFIANREAMLGHVEALRTLLAQIRQGGGLKAQERHTSRGKLLPRERI
Sbjct: 1   MATLHTQLNPRSPEFIANREAMLGHVEALRTLLAQIRQGGGLKAQERHTSRGKLLPRERI 60

Query: 61  NRLLDPGSPFLEISPLAAHDVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120
           NRLLDPGSPFLEISPLAAHDVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL
Sbjct: 61  NRLLDPGSPFLEISPLAAHDVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120

Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180
           TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ
Sbjct: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240
           IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK
Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240

Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKLGELQQRQPIAPLYSSDELYGVVSADAKQP 300
           ISGVADHYADSDEHALALARRSVANLNWRKLGELQQRQPIAPLYSSDELYGVVSADAKQP
Sbjct: 241 ISGVADHYADSDEHALALARRSVANLNWRKLGELQQRQPIAPLYSSDELYGVVSADAKQP 300

Query: 301 FDVREVIARLVDGSVFNEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360
           FDVREVIARLVDGSVFNEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI
Sbjct: 301 FDVREVIARLVDGSVFNEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360

Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420
           ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG
Sbjct: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420

Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480
           NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP
Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480

Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535
           ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM
Sbjct: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535


Lambda     K      H
   0.321    0.137    0.409 

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: 1187
Number of extensions: 23
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 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