GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Pseudomonas fluorescens FW300-N1B4

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf1N1B4_3986 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3986 Methylcrotonyl-CoA
           carboxylase carboxyl transferase subunit (EC 6.4.1.4)
          Length = 535

 Score = 1022 bits (2643), Expect = 0.0
 Identities = 513/535 (95%), Positives = 520/535 (97%)

Query: 1   MATLHTQLNPRSPEFIANREAMLGHVEALRTLLAQIRQGGGLKAQERHTSRGKLLPRERI 60
           MA LHTQLNPRS EF AN  AML  V+AL TLLAQ++QGGG KAQERHTSRGKLLPRERI
Sbjct: 1   MAILHTQLNPRSAEFAANSAAMLKQVDALHTLLAQVQQGGGPKAQERHTSRGKLLPRERI 60

Query: 61  NRLLDPGSPFLEISPLAAHDVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120
           NRLLDPGSPFLEIS LAA+ VYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL
Sbjct: 61  NRLLDPGSPFLEISQLAAYAVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120

Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180
           TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSA GIPQ
Sbjct: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMGIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240
           IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK
Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240

Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKLGELQQRQPIAPLYSSDELYGVVSADAKQP 300
           ISGVADHYA+SDEHALALARRSVANLNWRKLGELQQR PIAPLYSSDELYGVVSADAKQP
Sbjct: 241 ISGVADHYAESDEHALALARRSVANLNWRKLGELQQRTPIAPLYSSDELYGVVSADAKQP 300

Query: 301 FDVREVIARLVDGSVFNEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360
           FDVREVIARLVDGSVF+EFKALFGTTLVCGFAHLHGYP+AILANNGILFAEAAQKGAHFI
Sbjct: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360

Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420
           ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG
Sbjct: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420

Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480
           NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGH FSAEQEAEIKQP
Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHGFSAEQEAEIKQP 480

Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535
           ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVL LALSASLNAPIEPSRFGVFRM
Sbjct: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLALALSASLNAPIEPSRFGVFRM 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: 1133
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.

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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