Aligments for a candidate for pccA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for pccA in Dinoroseobacter shibae DFL-12

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate 3609096 Dshi_2485 pyruvate carboxylase (RefSeq)

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|FitnessBrowser__Dino:3609096 Dshi_2485 pyruvate carboxylase
           (RefSeq)
          Length = 1145

 Score =  374 bits (960), Expect = e-107
 Identities = 203/450 (45%), Positives = 276/450 (61%), Gaps = 9/450 (2%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARA-ADSY 60
           F K+L+ANRGEIA+RVMRA  ELG +TVAVY+E DK   H   ADEAY IG       +Y
Sbjct: 4   FQKILIANRGEIAIRVMRAANELGKKTVAVYAEEDKLCLHRFKADEAYKIGEGLGPVAAY 63

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L  + +I  A+ + ADAIHPGYG L+EN +F      +   ++GP A+ M  LG+K  AR
Sbjct: 64  LSIDEIIRVAKLSGADAIHPGYGLLSENPDFVDACVANGIAFIGPRAETMRALGDKASAR 123

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
            +  +A VPV+P T    D  + V+A A+  G+P+ +KA  GGGGRG++ +   DEV  +
Sbjct: 124 RVAIEAGVPVIPATEVLGDDMDKVRAEAEAIGFPLMLKASWGGGGRGMRPIFDPDEVADK 183

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
               +RE EA F N   Y+EK +   RH+EVQIL D  GN+ HL ERDCS+QRR+QKV+E
Sbjct: 184 VREGRREAEAAFGNGEGYLEKMITRARHVEVQILGDSMGNIYHLWERDCSVQRRNQKVVE 243

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFL--VEDGEFYFMEVNTRIQVEHTV 298
            AP+P LS   RE++ E  R+      Y  AGTVEFL  ++ GEF+F+EVN R+QVEHTV
Sbjct: 244 RAPAPYLSSSQREQLCELGRKICAHVNYECAGTVEFLMDMDTGEFFFIEVNPRVQVEHTV 303

Query: 299 TEEVTGLDVVKWQLRVAAGEEL-----DFSQDDVEIEGHSMEFRINAEAPEKEFAPATGT 353
           TEEVTG+D+V+ Q+ +A G+ L       SQ DV++ GH+++ RI  E P+  F P  G 
Sbjct: 304 TEEVTGIDIVRAQILIAEGKSLVEATGMASQYDVQLNGHAIQCRITTEDPQNNFIPDYGR 363

Query: 354 LSTYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE 412
           ++ Y    G+GIR+D      G  I   YDS++ K+       E  + R +RAL EF I 
Sbjct: 364 ITAYRGATGMGIRLDGGTAYSGAVITRYYDSLLEKVTAWAPTPEAAIARMDRALREFRIR 423

Query: 413 GLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442
           G+ T I F   +L    F    +TTK++DE
Sbjct: 424 GVSTNIAFVENLLKHPTFLNNQYTTKFIDE 453



 Score = 50.8 bits (120), Expect = 3e-10
 Identities = 43/136 (31%), Positives = 61/136 (44%), Gaps = 27/136 (19%)

Query: 466  EEGEVTERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQ 525
            E+GEV  + F  E+NG+  +V +  R A         AA+ A +P               
Sbjct: 1037 EDGEV--KVF-FELNGQPRQVRVPNRKA---------AASVAKRPKAEL----------- 1073

Query: 526  QVIEGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLV 585
                G+   V A M G + +V V  G  V+ GD +  +EAMKME  + AER   V  V V
Sbjct: 1074 ----GNPNHVGAPMPGVVASVAVQAGASVKEGDLLLTIEAMKMETGIHAERDAVVKAVHV 1129

Query: 586  GEGDSVDMGDVLLVLE 601
                 +D  D+L+ LE
Sbjct: 1130 TPAAQIDAKDLLVELE 1145


Lambda     K      H
   0.312    0.132    0.371 

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: 1444
Number of extensions: 60
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: 601
Length of database: 1145
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1103
Effective search space:   616577
Effective search space used:   616577
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 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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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, 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

GapMind for catabolism of small carbon sources