GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Magnetospirillum magneticum AMB-1

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_011383119.1 AMB_RS03475 methylcrotonoyl-CoA carboxylase

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



>NCBI__GCF_000009985.1:WP_011383119.1
          Length = 535

 Score =  747 bits (1928), Expect = 0.0
 Identities = 363/535 (67%), Positives = 431/535 (80%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M++I S I P S +F+AN    Q L  DL++ +AQ++ GGG   R RH  RGKL  R+RI
Sbjct: 1   MTVIKSSINPRSDEFKANAEATQGLVDDLKKVVAQVKMGGGPAMRERHIARGKLLPRERI 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
             L+D  S FLE   LAA+++Y ++V  AGI+ GIG + G+  MI+AND TVKGG+Y+PL
Sbjct: 61  RRLLDVGSPFLEFSQLAAWDMYSKDVMGAGIITGIGSINGQECMIVANDGTVKGGSYYPL 120

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           TVKKHLRAQ+IA+EN LPC+YLV+SGGA LP Q EVFPDRDHFGRIFYNQAQMSA GIPQ
Sbjct: 121 TVKKHLRAQDIAKENNLPCVYLVESGGANLPNQDEVFPDRDHFGRIFYNQAQMSALGIPQ 180

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           I+ V GSCTAGGAY+PAMSDE VIVK  GTIFLGGPPLVKAATGE V+AEELGGADVH R
Sbjct: 181 ISVVHGSCTAGGAYIPAMSDESVIVKNQGTIFLGGPPLVKAATGEVVSAEELGGADVHCR 240

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300
            SGV D++A DD  ALAI R IV +L   +  + ++  PE P YDP+EIYGI+P+D R+ 
Sbjct: 241 TSGVTDHYAQDDGHALAIARRIVGNLNRIKPTSLKMATPEEPLYDPKEIYGIIPKDRRKP 300

Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360
           YDVREVIARIVDGSRL EFK  YGTTLVCGFAHI G+PVGI+ANNGILFSESA KGAHF+
Sbjct: 301 YDVREVIARIVDGSRLDEFKQTYGTTLVCGFAHIWGYPVGIVANNGILFSESAQKGAHFV 360

Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420
           ELC  R IPL+FLQNITGFM+GK+YE GGIAKDGAK+VTAV+CA VP+FTVI+GGSFGAG
Sbjct: 361 ELCSQRGIPLIFLQNITGFMIGKKYEAGGIAKDGAKMVTAVACAKVPRFTVIMGGSFGAG 420

Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480
           NYGMCGRAYQPR L+MWP  R+SVMGG QAANV+  I++D + A+GQ    +E+E F AP
Sbjct: 421 NYGMCGRAYQPRMLYMWPTGRVSVMGGEQAANVMAQIKKDAMEAKGQSWPADEEEAFKAP 480

Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           I  +YE +GHPYYA ARLWDDG++DP ETR VLAL L+A+  AP++PT+FGVFRM
Sbjct: 481 IRDQYETQGHPYYAGARLWDDGLVDPAETRMVLALSLSASFNAPIEPTKFGVFRM 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: 1017
Number of extensions: 42
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