GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Sphingomonas koreensis DSMZ 15582

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ga0059261_4055 Ga0059261_4055 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)

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



>FitnessBrowser__Korea:Ga0059261_4055
          Length = 533

 Score =  712 bits (1839), Expect = 0.0
 Identities = 353/534 (66%), Positives = 417/534 (78%), Gaps = 6/534 (1%)

Query: 3   IIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRIDT 62
           ++ S + P    F+ N A++++LA  L   +AQ   GG  + R RH  RGKL  R+R++ 
Sbjct: 5   VLRSALSPEDEGFRTNAAHNRALAEKLHADVAQAALGGNEKSRERHTSRGKLLPRERVER 64

Query: 63  LIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPLTV 122
           L+DP S FLEIG LAA ++Y+ EVP AG++ GIGRV+GR  MI+ NDATVKGGTY+P+TV
Sbjct: 65  LLDPGSPFLEIGQLAACDMYEGEVPGAGMIAGIGRVSGRQCMIVCNDATVKGGTYYPMTV 124

Query: 123 KKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQIA 182
           KKHLRAQEIA  NRLPCIYLVDSGGA LP Q+EVFPD++HFGRIF+NQA MSA+GIPQIA
Sbjct: 125 KKHLRAQEIAEANRLPCIYLVDSGGANLPHQAEVFPDKEHFGRIFFNQANMSAKGIPQIA 184

Query: 183 CVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTRIS 242
           CVMGSCTAGGAYVPAMSDE VIV+  GTIFL GPPLVKAATGEE++AE+LGG D+H R S
Sbjct: 185 CVMGSCTAGGAYVPAMSDESVIVRNQGTIFLAGPPLVKAATGEEISAEDLGGGDLHGRKS 244

Query: 243 GVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQSYD 302
           GV D+ A +D  AL IVRDIV+HL   +  +  + DP PP++D  E+YGI+P D R  YD
Sbjct: 245 GVVDHVAENDEHALTIVRDIVSHLPRDRTPDVAILDPRPPKFDAEELYGIVPTDVRAPYD 304

Query: 303 VREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFIEL 362
           V EVIARIVDGS  HEFK  YG+TLVCGFAHI G PV ILANNG+LFSESA+KGAHFIEL
Sbjct: 305 VHEVIARIVDGSEFHEFKAPYGSTLVCGFAHIWGMPVAILANNGVLFSESAVKGAHFIEL 364

Query: 363 CCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAGNY 422
            C R IPL+FLQNI+GFMVG +YE  GIAK GAKLVTAV+ A+VPK TV+IGGSFGAGNY
Sbjct: 365 ACQRRIPLLFLQNISGFMVGGKYEAEGIAKHGAKLVTAVATASVPKITVLIGGSFGAGNY 424

Query: 423 GMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAPIL 482
           GMCGRAY PR L+ WPN+RISVMGG QAA+VL T+ RD         TPE+ E F API 
Sbjct: 425 GMCGRAYSPRFLFSWPNSRISVMGGEQAASVLATVHRD-----ADSWTPEQAETFKAPIR 479

Query: 483 AKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQP-TRFGVFRM 535
            KYE EG+P++A+ARLWDDG+IDP +TR VL L  AA   APV+  TRFGVFRM
Sbjct: 480 QKYEDEGNPWHATARLWDDGIIDPAQTRDVLGLAFAATLNAPVEEGTRFGVFRM 533


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: 962
Number of extensions: 40
Number of successful extensions: 4
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: 533
Length adjustment: 35
Effective length of query: 500
Effective length of database: 498
Effective search space:   249000
Effective search space used:   249000
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