GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03840 H281DRAFT_03840 urea carboxylase

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



>FitnessBrowser__Burk376:H281DRAFT_03840
          Length = 1199

 Score =  328 bits (840), Expect = 9e-94
 Identities = 173/439 (39%), Positives = 268/439 (61%), Gaps = 3/439 (0%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F ++L+ANRG IA R+L+ ++E+ +T ++V+SEAD+ + H   A  A+ +G  PA  +YL
Sbjct: 2   FEKILIANRGAIACRILRTLRELNVTGVSVFSEADRASRHVSEAPIAHELGDGPAAMTYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           +   I++ A    V AIHPGYGFLSENA F EA E AGI FIGP+   +R    K   + 
Sbjct: 62  DSTKILEIARCEGVQAIHPGYGFLSENAAFGEACEAAGIAFIGPTPAQLRAFGLKHTARE 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           +A   GVP   G+ G +  +  AL  AE IGYP+M+K+ +GGGG+G+    + D+L   +
Sbjct: 122 IAGEQGVPMLNGT-GLLEDLPAALNAAESIGYPVMLKSTAGGGGIGMRVCWHADELSAHF 180

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
           +  KRL    F  + +F+EKY    RH+E Q+ GD  G+ +    R+C++QRRNQK++EE
Sbjct: 181 DAVKRLGENNFSDSGVFLEKYIERARHLEVQVFGDGKGDAIALGVRDCSVQRRNQKVLEE 240

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
            P+P L     +++ +  +K  K ++Y + GT E  +   ++ FYFLE+N RLQVEH  T
Sbjct: 241 TPAPCLPEGIAQALCDAAVKLAKAVDYRSAGTVEFVYDSTAQQFYFLEVNTRLQVEHGVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY- 362
           E ++ +DLV+  I+LAAG   P ++   +   RG AI+ R+ AED   +F  S G +T+ 
Sbjct: 301 EQVWGVDLVRWMIELAAGTLAPLNELAASLTPRGHAIQARLYAEDPGRDFIPSPGLLTHV 360

Query: 363 -YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421
            + +  G  +R+D+ IESG  VPPY+D +++K+I +  +RE A  A   AL + +I G++
Sbjct: 361 AFPQADGSALRIDTWIESGCEVPPYFDPMLAKIIAWSPTREEARHALNDALQNTRIFGVE 420

Query: 422 TTIELYKWIMQDPDFQEGK 440
           T  +  + I+ D  F  G+
Sbjct: 421 TNRDYLRQILDDEPFASGE 439


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: 1295
Number of extensions: 56
Number of successful extensions: 3
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: 1199
Length adjustment: 41
Effective length of query: 468
Effective length of database: 1158
Effective search space:   541944
Effective search space used:   541944
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: 55 (25.8 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