GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Corynebacterium deserti GIMN1.010

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 WP_053544274.1 CDES_RS03395 pyruvate carboxylase

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_001277995.1:WP_053544274.1
          Length = 1140

 Score =  379 bits (974), Expect = e-109
 Identities = 222/523 (42%), Positives = 315/523 (60%), Gaps = 21/523 (4%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARA-ADSY 60
           F K+LVANRGEIAVR  RA  E G  TVA+Y   D+   H  +A EA  IG   +   +Y
Sbjct: 12  FKKILVANRGEIAVRAFRAAYETGAATVAIYPREDRGSFHRSFASEAVRIGQEGSPVKAY 71

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           LD + +I AA+K  ADAI+PGYGFL+ENA+ AR+  ++  T++GP+ + ++  G+K++A 
Sbjct: 72  LDIDEIIGAAKKVKADAIYPGYGFLSENAQLARECAENGITFIGPTPEVLDLTGDKSRAV 131

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
           +  ++A +PV+  +T P+ S +D+   A+   YP+ +KA  GGGGRG++ V   +++   
Sbjct: 132 TAAKEAGLPVLAEST-PSRSIDDIVKSAEGQTYPIFVKAVAGGGGRGMRFVEKPEDLRKL 190

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
              A RE EA F + +VYVE+ +  P+HIEVQIL D  G+V HL ERDCSLQRRHQKV+E
Sbjct: 191 ATEASREAEAAFGDGAVYVERAVINPQHIEVQILGDHTGDVIHLFERDCSLQRRHQKVVE 250

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLV-EDGEFYFMEVNTRIQVEHTVT 299
            AP+  L  +LR+RI   A +  R+  Y  AGTVEFLV E G   F+E+N RIQVEHTVT
Sbjct: 251 IAPAQHLDPELRDRICADAVKFCRSIGYQGAGTVEFLVDEKGNHVFIEMNPRIQVEHTVT 310

Query: 300 EEVTGLDVVKWQLRVAAG---EELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLST 356
           EEVT +D+VK Q+R+AAG   ++L  +QD ++  G +++ RI  E P   F P TGT++ 
Sbjct: 311 EEVTEVDLVKAQMRLAAGATLKDLGLTQDKIKTHGAALQCRITTEDPNNGFRPDTGTITA 370

Query: 357 YDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRT 416
           Y  PGG G+R+D A + G EI   +DSM+ K+   GSD    + RA+RAL EF + G+ T
Sbjct: 371 YRSPGGAGVRLDGAAQLGGEITAHFDSMLVKMTCRGSDFATAVARAQRALAEFTVSGVAT 430

Query: 417 VIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVTERTFT 476
            I F R +L +E F      T ++ +   P  ++A      P A   D+E+G + +    
Sbjct: 431 NIGFLRALLREEDFTTKRIATGFIAD--HPHLLQA------PPA---DDEQGRILDYLAD 479

Query: 477 VEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREE 519
           V VN    E   +     A PL    A      P G R R ++
Sbjct: 480 VTVNKPHGERPKD----IAAPLDKLPAIKDLPLPRGSRDRLKQ 518



 Score = 57.0 bits (136), Expect = 4e-12
 Identities = 37/106 (34%), Positives = 56/106 (52%), Gaps = 5/106 (4%)

Query: 499  GGASAAASASKPSGPRKRREESDEGGQQVIEGDGES----VAAEMQGTILAVEVDEGDDV 554
            G  +  A+ +    P + R+ S E      E    S    VAA   G ++ V V EGD+V
Sbjct: 1035 GMRNVVANVNGQIRPMRVRDRSVESVTATAEKADPSNKGHVAAPFAG-VVTVTVAEGDEV 1093

Query: 555  EPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLVL 600
            + GD V I+EAMKME  + A   GT+ +V+V     V+ GD+++V+
Sbjct: 1094 KAGDAVAIIEAMKMEATITAHADGTIQRVVVPAATKVEGGDLIVVI 1139


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: 1406
Number of extensions: 58
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 601
Length of database: 1140
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1098
Effective search space:   613782
Effective search space used:   613782
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 24 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