GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Kocuria flava HO-9041

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_058857839.1 AS188_RS04435 methylcrotonoyl-CoA carboxylase

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



>NCBI__GCF_001482365.1:WP_058857839.1
          Length = 535

 Score =  692 bits (1787), Expect = 0.0
 Identities = 338/535 (63%), Positives = 409/535 (76%)

Query: 1   MSIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRI 60
           M ++ + ++P +  F+AN A    LAA+L  RL ++ +GG    R RH  RGKL  R+R+
Sbjct: 1   MQVLGTAVEPEAAAFRANAAAQAELAAELGRRLERVARGGPEASRERHTARGKLLPRERV 60

Query: 61  DTLIDPDSSFLEIGALAAYNVYDEEVPAAGIVCGIGRVAGRPVMIIANDATVKGGTYFPL 120
           D L+D  S FLEIGALAA  +Y++E PAAG++ GIG V GR  M++ NDATVKGGTY+P+
Sbjct: 61  DRLLDAGSPFLEIGALAAEGMYEDECPAAGLIAGIGLVHGRQAMVVCNDATVKGGTYYPM 120

Query: 121 TVKKHLRAQEIARENRLPCIYLVDSGGAYLPLQSEVFPDRDHFGRIFYNQAQMSAEGIPQ 180
           TVKKHLRAQEIA ENRLPC+YLVDSGGAYLPLQ EVFPDR+HFGRIFY+QA++SA GIPQ
Sbjct: 121 TVKKHLRAQEIALENRLPCVYLVDSGGAYLPLQDEVFPDREHFGRIFYHQARLSAAGIPQ 180

Query: 181 IACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGADVHTR 240
           +A V+GSCTAGGAYVPAMSDE VIV+  GT+FLGGPPLV+AATGEEVTAEELGG ++H  
Sbjct: 181 LAAVLGSCTAGGAYVPAMSDETVIVRHQGTVFLGGPPLVRAATGEEVTAEELGGGELHAH 240

Query: 241 ISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEPPRYDPREIYGILPRDFRQS 300
            SGV D+ A +D  AL I+RD+VA L       W +  PE P     ++ G +P D    
Sbjct: 241 TSGVVDHLAENDEHALQILRDVVATLPQPAPRAWPVTAPEAPAVAEEQLPGAVPVDPNTG 300

Query: 301 YDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALKGAHFI 360
           YDVREVIAR+VDGSR  EFK  YGTTLV GFA + G PVGI+ANNG+LF+ESALKGAHF+
Sbjct: 301 YDVREVIARLVDGSRFGEFKAGYGTTLVTGFARLHGHPVGIVANNGVLFAESALKGAHFV 360

Query: 361 ELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGGSFGAG 420
           +LC  R IPL+FLQNITGFMVG+ YE GGIAK GAK+VTAV+   VPK TV+IGGSFGAG
Sbjct: 361 QLCDQRGIPLLFLQNITGFMVGRDYEAGGIAKHGAKMVTAVATTRVPKLTVVIGGSFGAG 420

Query: 421 NYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQERFMAP 480
           NY MCGRA+ PR L++WP ARISVMGG QAA+VL T+R D L ARGQ+  P  +E FMAP
Sbjct: 421 NYSMCGRAFSPRFLFLWPQARISVMGGAQAASVLATVRADRLAARGQEWDPAGREAFMAP 480

Query: 481 ILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEAPVQPTRFGVFRM 535
           I A+YE +G+P+YA+ARLWDDGVI P +TR VL L L   +  P+    FG+FRM
Sbjct: 481 IRAQYEAQGNPWYATARLWDDGVIAPADTREVLGLALEVCSRTPLPEPSFGLFRM 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: 987
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: 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 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