GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccB in Sinorhizobium meliloti 1021

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate SM_b21122 SM_b21122 methylcrotonoyl-CoA carboxylase non-biotinylated subunit protein

Query= metacyc::MONOMER-17283
         (535 letters)



>lcl|FitnessBrowser__Smeli:SM_b21122 SM_b21122 methylcrotonoyl-CoA
           carboxylase non-biotinylated subunit protein
          Length = 535

 Score =  721 bits (1861), Expect = 0.0
 Identities = 349/535 (65%), Positives = 419/535 (78%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M+++ SHI P+S +F+AN A      A + + +     GGG   R RH  RGKL  RDR+
Sbjct: 1   MTVLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRL 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
            TLIDP + FLE+GA AAY +Y+++ P AG++ GIGR++ R  MI+ ND TVKGGTY+PL
Sbjct: 61  ATLIDPGTPFLEVGATAAYGMYNDDAPGAGLITGIGRISARECMIVCNDPTVKGGTYYPL 120

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           TVKKHLRAQEIA ENRLPC+YLVDSGGA LP Q EVFPDRDHFGRIFYNQA MSA GIPQ
Sbjct: 121 TVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAGIPQ 180

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           IA VMGSCTAGGAYVPAMSDE +IV+  GTIFL GPPLV+AATGE V+AE+LGGADVHTR
Sbjct: 181 IAVVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADVHTR 240

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300
           +SGVAD+ A DD  ALA+ R  V+ L   +    E  +PEPP YDP EI GI+P D +  
Sbjct: 241 LSGVADHLARDDAHALALARRAVSALNREKPWTVERIEPEPPLYDPEEIAGIVPADLKTP 300

Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360
           Y++REVIAR+VDGSR  EFK R+GTTLVCGFAH+ G PVGI+ANNG+LFSESA+KGAHF+
Sbjct: 301 YEIREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVKGAHFV 360

Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420
           ELC  R IPLVFLQNITGFMVG++YE  GIAK GAKLVTAV+   VPK T+++GGSFGAG
Sbjct: 361 ELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGGSFGAG 420

Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480
           NYGMCGRA+ PR LW WPN+RISVMGG QAA VL ++R + L+  G+  + EE+ RF  P
Sbjct: 421 NYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEARFRQP 480

Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           +L  +E++ HP YASARLWDDGVIDP ++R VLAL L+AA  AP++ TRFG+FRM
Sbjct: 481 VLDLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLFRM 535


Lambda     K      H
   0.322    0.139    0.423 

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: 966
Number of extensions: 37
Number of successful extensions: 3
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 (21.9 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 paper from 2022 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