GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuD in Burkholderia phytofirmans PsJN

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate BPHYT_RS23265 BPHYT_RS23265 methylcrotonoyl-CoA carboxylase

Query= reanno::SB2B:6937191
         (535 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS23265 BPHYT_RS23265
           methylcrotonoyl-CoA carboxylase
          Length = 535

 Score =  822 bits (2124), Expect = 0.0
 Identities = 392/535 (73%), Positives = 455/535 (85%)

Query: 1   MTQLTSRVNPRSDEFKQKHDAMAALVADLKDKLAHIEQGGGLVAMERHLSRGKLAPRARV 60
           M  + S++NPRSD+F+    A+ ALVADL+ K+  +  GGG  A ++H  RGKL PR R+
Sbjct: 1   MPIIESKLNPRSDDFRANAAALEALVADLRAKVEKLALGGGQAARDKHTGRGKLLPRERI 60

Query: 61  EKLLDPGSPFLELSQFAAFEVYDEDVPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPI 120
           EKLLDPG+PFLE SQ AA+ +Y++D P AG+I GIGR++G EC+I+ NDATVKGGTYYPI
Sbjct: 61  EKLLDPGTPFLEFSQLAAYGMYNDDAPGAGVITGIGRIAGQECVIVCNDATVKGGTYYPI 120

Query: 121 TVKKHLRAQAIAERCHLPCIYLVDSGGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQ 180
           TVKKH+RAQ IA   HLPC+YLVDSGGANLP QD+VFPDRDHFGRIFFNQA +SA GIPQ
Sbjct: 121 TVKKHVRAQEIAAENHLPCVYLVDSGGANLPNQDDVFPDRDHFGRIFFNQANLSAAGIPQ 180

Query: 181 IAVVMGLCTAGGAYVPAMADESIIVREQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTK 240
           IAVVMG CTAGGAYVPAM+DESIIV+ QGTIFL GPPLVKAATGE VSAE+LGGGDVHT+
Sbjct: 181 IAVVMGSCTAGGAYVPAMSDESIIVKNQGTIFLGGPPLVKAATGEVVSAEDLGGGDVHTR 240

Query: 241 ISGVADHLAQNDEHALELARKAVSRLNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKP 300
           +SGV DHLAQND HAL +AR  V  LN  KQV L L + KPP+YD+  +YG++  D +KP
Sbjct: 241 LSGVVDHLAQNDAHALGIARSIVGNLNRSKQVPLALQEPKPPRYDVKSMYGVIPVDTRKP 300

Query: 301 FDVKEVIARIVDDSDFDEFKANYGTTLVCGFARIHGYPVGIVANNGILFSESAQKGAHFI 360
           FD++EVIARIVDDS FDEFKA YGTTLVCGFA I G+PVGI+ANNGILFSESA KGAHFI
Sbjct: 301 FDIREVIARIVDDSAFDEFKARYGTTLVCGFAHIWGHPVGIIANNGILFSESALKGAHFI 360

Query: 361 ELCCQRKIPLVFLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAG 420
           ELCCQRKIPLVFLQNITGFMVG+KYE+EGIA++GAKMVTAV+ A VPKFTV+IGGS+GAG
Sbjct: 361 ELCCQRKIPLVFLQNITGFMVGRKYENEGIARNGAKMVTAVATAKVPKFTVIIGGSFGAG 420

Query: 421 NYGMCGRAFEPTLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAP 480
           NYGMCGRA+ P  +WMWPNARISVMGGEQAA VLATV++DG+  KG + SAEEE  FK P
Sbjct: 421 NYGMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVKRDGIEGKGGSWSAEEEEAFKQP 480

Query: 481 IIAQYDKEGHPYHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGVFRM 535
           I  QY+ +GHPY+ASARLWDDG+IDPAQTRDVLGL +SA +NAPIE+TRFGVFRM
Sbjct: 481 IREQYEHQGHPYYASARLWDDGVIDPAQTRDVLGLGLSATMNAPIEDTRFGVFRM 535


Lambda     K      H
   0.320    0.137    0.405 

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: 1033
Number of extensions: 52
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 (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