Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS25130 RR42_RS25130 pyruvate carboxylase

Query= reanno::Dino:3607308
         (681 letters)



>FitnessBrowser__Cup4G11:RR42_RS25130
          Length = 1167

 Score =  382 bits (981), Expect = e-110
 Identities = 205/481 (42%), Positives = 290/481 (60%), Gaps = 42/481 (8%)

Query: 3   KKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPAN-QSYI 61
           K +LIANR EIA RV++ A +M I+TVAIYS  DR ALH   ADE+  +G       +Y+
Sbjct: 7   KSLLIANRSEIAIRVMRAAAEMNIRTVAIYSKEDRLALHRFKADESYLVGEGKKPLAAYL 66

Query: 62  VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121
            ID ++   RQ   +A+HPGYGFLSEN  FA+A+   G+ +IGP    +  +G+K+ ++ 
Sbjct: 67  DIDDILRIARQAKVDAIHPGYGFLSENPDFAQAVMDAGIRWIGPSPEVMRKLGNKVAARN 126

Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGF 181
            A EA V  +P    L  D DE  +++  IGYP+M+KAS GGGG+GMR+  N+ +     
Sbjct: 127 AAIEAGVPVMPATDPLPRDLDECKRLAAGIGYPLMLKASWGGGGRGMRMLENEQDLETAL 186

Query: 182 QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEE 241
            +++ EA ++FG+D +++EK V   RH+E+Q L D HGN ++L ER+C++QRRNQKVVE 
Sbjct: 187 PAARREALSAFGNDEVYVEKLVRNARHVEVQALGDAHGNLVHLYERDCTVQRRNQKVVER 246

Query: 242 APSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR-NFYFLEMNTRLQVEHPVT 300
           AP+P+LD+A R A+ + +  L +AVGY  AGT+EF++D D   FYF+E+N R+QVEH VT
Sbjct: 247 APAPYLDDAGRAALCDAAMRLMRAVGYTHAGTIEFLMDADSGQFYFIEVNPRIQVEHTVT 306

Query: 301 ELITGVDLVEQMIRVAAGEKLPMT-------------------QDDVTLTGWAIENRLYA 341
           EL+TGVD+V+  IR+  G  + MT                   Q  ++L G A++ R+  
Sbjct: 307 ELVTGVDIVKAQIRITEGGHIGMTENTRDADGKIVVRAAGVPEQAGISLNGHALQCRITT 366

Query: 342 EDPYRNFLPSIGRLTRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTG-VYEGGEISM 400
           EDP   FLP  GRL+ YR     AAG                  VR D G  Y G  I+ 
Sbjct: 367 EDPENGFLPDYGRLSAYRS----AAG----------------FGVRLDAGTAYGGAVITP 406

Query: 401 YYDPMIAKLCTWGPDRPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAF 460
           YYD ++ K+ TW P  P +I  M  AL  F + G+  NL F+  V++HP F  G++TT F
Sbjct: 407 YYDSLLVKVTTWAPTAPESIRRMDRALREFRIRGVASNLQFLENVINHPAFRSGDVTTRF 466

Query: 461 I 461
           I
Sbjct: 467 I 467



 Score = 50.4 bits (119), Expect = 5e-10
 Identities = 23/71 (32%), Positives = 38/71 (53%)

Query: 609  PDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATVTKINAGAG 668
            P     +  PMPG +V + V+ G  V  G  L  +EAMKME  + A++   +  ++   G
Sbjct: 1094 PGNPLHVAAPMPGAIVTVAVQPGQRVAAGTTLLALEAMKMETHIAADRDCEIAAVHVQQG 1153

Query: 669  DSLAVDDVIME 679
            D +A  D+++E
Sbjct: 1154 DRVAAKDLLIE 1164


Lambda     K      H
   0.318    0.134    0.392 

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: 1839
Number of extensions: 84
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: 2
Length of query: 681
Length of database: 1167
Length adjustment: 43
Effective length of query: 638
Effective length of database: 1124
Effective search space:   717112
Effective search space used:   717112
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources