GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Burkholderia phytofirmans PsJN

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 BPHYT_RS25975 BPHYT_RS25975 urea carboxylase

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



>FitnessBrowser__BFirm:BPHYT_RS25975
          Length = 1203

 Score =  342 bits (876), Expect = 6e-98
 Identities = 189/445 (42%), Positives = 273/445 (61%), Gaps = 5/445 (1%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F +VL+ANRGEIA RV++ +K +G+ ++AVYSEAD++A+H   ADEA  IG A A  SYL
Sbjct: 3   FRKVLIANRGEIACRVIRTLKRLGIASVAVYSEADRHAMHVMLADEAVCIGPALAAQSYL 62

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
           N   I+DAA     DA+HPGYGFLSENA FA+A + AGI FIGP+ + MR+   K   + 
Sbjct: 63  NSAAILDAARACGADAVHPGYGFLSENAAFAQACDDAGIRFIGPTPQHMREFGLKHTARE 122

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           LA    V   PG+ G +  +  AL+ AE IGYP+M+K+ +GGGG+G++   +  QL  V+
Sbjct: 123 LAQANDVALLPGT-GLLPDVSAALREAESIGYPVMLKSTAGGGGIGMSLCRDAAQLEGVF 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
               RL    F  A +++EK+  N RHIE Q+ GD  G  +   ER+C++QRRNQK+IEE
Sbjct: 182 ASVARLGEANFANAGVYVEKFVENARHIEVQVFGDGKGGVISLGERDCSVQRRNQKVIEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
            P+P L   ER ++    ++  + + Y + GT E  F   +R FYFLE+N RLQVEH  T
Sbjct: 242 TPAPGLTHAERSALHASAVRLAQAVKYKSAGTVEFVFDADTRRFYFLEVNTRLQVEHCVT 301

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E I  IDLV+  I+ A GE  P   + L    +G +I+ R+ AED    F  S+G +T+ 
Sbjct: 302 EEITGIDLVEWMIREAEGELAPL--DTLATVPQGASIQVRLYAEDPHKQFQPSAGVLTHV 359

Query: 364 REPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTT 423
                   RVD+ ++SG+ V  +YD L++KLIV GE+RE  + A   AL   ++ GI+T 
Sbjct: 360 --AFAADARVDTWVDSGTEVSAFYDPLLAKLIVKGETREAGLAALRAALEQTQLYGIETN 417

Query: 424 IELYKWIMQDPDFQEGKFSTSYISQ 448
           ++  + I     F  G+ +T+++ +
Sbjct: 418 LDYLRAIAGSATFARGEQTTAFLGR 442


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: 1279
Number of extensions: 56
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 509
Length of database: 1203
Length adjustment: 41
Effective length of query: 468
Effective length of database: 1162
Effective search space:   543816
Effective search space used:   543816
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