GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Pseudomonas putida KT2440

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate PP_4065 PP_4065 methylcrotonyl-CoA carboxylase biotin-containing subunit beta

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



>FitnessBrowser__Putida:PP_4065
          Length = 535

 Score =  720 bits (1859), Expect = 0.0
 Identities = 354/535 (66%), Positives = 417/535 (77%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M+ +H+ I P S +F  N A        LR  LAQ+ QGGG + + RH  RGKL  R+RI
Sbjct: 1   MATLHTQINPRSAEFAVNSAAMLEQVQALRGLLAQVAQGGGPKAQERHTSRGKLLPRERI 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
           D L+DP S FLEIG LAA+ VY E+VPAAG++ GIGRV G   MI+ANDATVKGG+Y+PL
Sbjct: 61  DRLLDPGSPFLEIGQLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           TVKKHLRAQ IA +NRLPCIYLVDSGGA LP Q EVFPDR+HFGRIF+NQA MSA+GIPQ
Sbjct: 121 TVKKHLRAQTIALQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           IA VMGSCTAGGAYVPAM+DE ++V+   TIFL GPPLVKAATGE V+AE+LGGADVH R
Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCR 240

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300
            SGVAD++A++D  ALAI R  VA+L   +    +   P  P Y   E+YG++P D +Q 
Sbjct: 241 TSGVADHYADNDEHALAIARRSVANLNWHKLGKLQRLAPVAPLYAADELYGVVPADAKQP 300

Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360
           +DVREVIAR+VDGS   EFK  +GTTLVCGFAH+ G+PV ILANNGILF+E+A KGAHFI
Sbjct: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360

Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420
           EL C R IPL+FLQNITGFMVGK+YE GGIAK GAKLVTAV+CA VPKFTVIIGGSFGAG
Sbjct: 361 ELACQRGIPLLFLQNITGFMVGKKYEEGGIAKHGAKLVTAVACAQVPKFTVIIGGSFGAG 420

Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480
           NYGMCGRAY PR LWMWPNARI VMG  QAA VL  ++R+     GQ  + E++ R   P
Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLAQVKREQSERSGQPFSAEDEARLKQP 480

Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           IL +YE++GHPYY+SARLWDDGVIDP +TR VL L L+AA  AP++ +RFG+FRM
Sbjct: 481 ILDQYERQGHPYYSSARLWDDGVIDPAQTRDVLGLALSAALNAPIEQSRFGIFRM 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: 954
Number of extensions: 32
Number of successful extensions: 2
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:

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