GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Brevibacterium jeotgali SJ5-8

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_101586893.1 BJEO58_RS00860 methylcrotonoyl-CoA carboxylase

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



>NCBI__GCF_900169175.1:WP_101586893.1
          Length = 536

 Score =  688 bits (1775), Expect = 0.0
 Identities = 344/540 (63%), Positives = 410/540 (75%), Gaps = 9/540 (1%)

Query: 1   MSIIHSHIQPN-SPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDR 59
           M  I S + P  SP  QA    H  L  +L +R A    GG    R+RH +RGKL  RDR
Sbjct: 1   MRSIGSPVDPQTSPHTQA----HAQLLDELGQRTAATALGGSESSRQRHLDRGKLLPRDR 56

Query: 60  IDTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFP 119
           ++ L+DP S FLE  ALAA  +YD+  P AGI+ G+G ++GR  +I+ANDATVKGGTY+P
Sbjct: 57  VEGLLDPGSPFLEFSALAANGMYDDASPGAGIITGMGLISGRLCVIVANDATVKGGTYYP 116

Query: 120 LTVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIP 179
           +TVKKHLRAQEIA++N LPC+YLVDSGGA LP Q +VFPDRDHFGRIF+NQA +SA GIP
Sbjct: 117 VTVKKHLRAQEIAQQNNLPCLYLVDSGGANLPNQDDVFPDRDHFGRIFFNQATLSAAGIP 176

Query: 180 QIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHT 239
           Q+A VMGSCTAGGAYVPAM+DE VIV   GTIFLGGPPLVKAATGE VTAEELGG  +H+
Sbjct: 177 QLAAVMGSCTAGGAYVPAMADESVIVNEQGTIFLGGPPLVKAATGEVVTAEELGGGALHS 236

Query: 240 RISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQ 299
           R SGV D+ A +D  AL I+RDIVA  GPR    W+  +P+ P +DP EI  ++P D + 
Sbjct: 237 RTSGVTDHLAANDEHALEILRDIVATFGPRHAPAWDRAEPQAPAHDPDEITAVVPVDSKV 296

Query: 300 SYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHF 359
            YDVREVIAR+VD S  HEFK  YGTTLV GFA I+G PVGI+ANNGILF ESA+KGAHF
Sbjct: 297 PYDVREVIARLVDASEFHEFKAEYGTTLVTGFARIDGHPVGIIANNGILFGESAMKGAHF 356

Query: 360 IELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGA 419
           IELC  R+ PLVFLQNI+GFMVG+ YE  GIAK GAK+V AV+ A VPKFTV+IGGSFGA
Sbjct: 357 IELCDQRSTPLVFLQNISGFMVGRDYEAAGIAKHGAKMVNAVATARVPKFTVVIGGSFGA 416

Query: 420 GNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMA 479
           GNY MCGRAY PR LWMWPNARISVMGG QAA+VL T++RD +  RG+D + E++E F  
Sbjct: 417 GNYSMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVKRDQIAGRGEDWSTEDEESFKD 476

Query: 480 PILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAA----AEAPVQPTRFGVFRM 535
           PI  +YE +G+PYY++ARLWDDG+I P +TRRVLAL L AA     E P+  + +GVFRM
Sbjct: 477 PIRQQYEDQGNPYYSTARLWDDGIIAPADTRRVLALALEAARFSPLERPLAASGYGVFRM 536


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: 46
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: 536
Length adjustment: 35
Effective length of query: 500
Effective length of database: 501
Effective search space:   250500
Effective search space used:   250500
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 24 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