GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Pseudomonas simiae WCS417

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate GFF583 PS417_02965 acetyl-CoA carboxylase

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__WCS417:GFF583
          Length = 453

 Score =  377 bits (968), Expect = e-109
 Identities = 199/445 (44%), Positives = 289/445 (64%), Gaps = 6/445 (1%)

Query: 6   RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65
           +VL+ANRGEIA R+L+A KE G+  +AVYS AD   +H K ADE+  IG   A +SYL +
Sbjct: 10  KVLIANRGEIALRILRACKEEGIKTVAVYSTADTELMHVKLADESICIGPPLATNSYLKV 69

Query: 66  EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125
            +II AAE    D IHPGYGFL+ENA+FAE VEK+G  FIGP +E +R + DK+  K   
Sbjct: 70  SNIIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFAFIGPKAETIRLMGDKVSAKDAM 129

Query: 126 NMAGVPTAPGSDGPVTSIDE-ALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWE 184
             AGVPT PGSDGP+   +E AL++  ++GYP+++KAA GGGG G+  V  ++ L++  +
Sbjct: 130 IAAGVPTVPGSDGPLPEDEETALRIGREVGYPVIIKAAGGGGGRGMRVVHKEEDLIEAAK 189

Query: 185 RNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEA 244
           + +  A   FG   +++EKY  NPRH+E Q++ D  G+ +   +R+C++QRR+QK++EEA
Sbjct: 190 QTRSEAGAWFGNPMVYLEKYLTNPRHVEVQVLSDGQGHAIHLGDRDCSLQRRHQKVLEEA 249

Query: 245 PSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTE 304
           P+P L  + R+ +    +K    INY   GTFE  +   +  FYF+E+N R+QVEHP +E
Sbjct: 250 PAPGLDEKARQEVLARCVKACIDINYRGAGTFEFLYE--NGRFYFIEMNTRVQVEHPVSE 307

Query: 305 LIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYR 364
           ++  ID+VK  + +AAG  L F+Q+D+  ++ G ++E RINAED    F  S G V ++ 
Sbjct: 308 MVTGIDIVKEMLSIAAGNPLSFTQDDV--KMHGHSLECRINAEDP-KTFIPSPGLVKHFH 364

Query: 365 EPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTI 424
            P G GVRVDS + SG  VP  YDSL+ KLI +G +R+ A+     AL +  + GIKT I
Sbjct: 365 APGGNGVRVDSHLYSGYKVPSNYDSLIGKLITWGATRDEAMARMRNALDEIVVDGIKTNI 424

Query: 425 ELYKWIMQDPDFQEGKFSTSYISQK 449
            L++ +++D  F EG  +  Y+  K
Sbjct: 425 PLHRDLVRDEGFCEGGVNIHYLEHK 449


Lambda     K      H
   0.317    0.135    0.385 

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: 529
Number of extensions: 17
Number of successful extensions: 5
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: 509
Length of database: 453
Length adjustment: 34
Effective length of query: 475
Effective length of database: 419
Effective search space:   199025
Effective search space used:   199025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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