GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3609096
          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:

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