GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25975 BPHYT_RS25975 urea
           carboxylase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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