GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_4056 Ga0059261_4056 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Korea:Ga0059261_4056
          Length = 626

 Score =  346 bits (888), Expect = 1e-99
 Identities = 186/448 (41%), Positives = 282/448 (62%), Gaps = 10/448 (2%)

Query: 7   VLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNIE 66
           +L+ANRGEIA R+++  +++G+  +AVYS+AD +A+H + AD+A +IG + A +SYL  E
Sbjct: 5   LLIANRGEIACRIIRTARKLGIRTVAVYSDADAHALHVREADQAVHIGGSQARESYLVGE 64

Query: 67  HIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLAN 126
            +I AA++   +AIHPGYGFLSENA+FAEAV  AG+ ++GP+ + +R +  K   K+L  
Sbjct: 65  RVIAAAKETGAEAIHPGYGFLSENADFAEAVVAAGLIWVGPNPDSIRAMGLKDAAKKLMQ 124

Query: 127 MAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWERN 186
            A VP  PG  G   S+D   + A+KIGYP+++KA +GGGG G+ RVD  +   D     
Sbjct: 125 DARVPVTPGYLGEDQSLDRLQREADKIGYPVLIKAVAGGGGKGMRRVDVAEDFADALASC 184

Query: 187 KRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPS 246
           +R A  +FG   + IEKY + PRHIE Q+ GD +GN V  +ER+C++QRR+QK+IEEAP+
Sbjct: 185 QREAASSFGDDRVLIEKYILAPRHIEVQVFGDSHGNIVHLFERDCSMQRRHQKVIEEAPA 244

Query: 247 PALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRD-----FYFLELNKRLQVEHP 301
           P +    R ++ E  +K  + +NY   GT E   +D S+       +F+E+N RLQVEHP
Sbjct: 245 PGMDKSARFAVCEAAVKAARAVNYVGAGTIE-FIADASQGLHADRIWFMEMNTRLQVEHP 303

Query: 302 TTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVT 361
            TE I  +DLV+ Q+++A+GE LP  QE++   + G AIE R+ AED    F  S+G + 
Sbjct: 304 VTEAITGVDLVEWQLRVASGEPLPLRQEEI--AISGHAIEARLYAEDPARGFLPSTGKLE 361

Query: 362 YYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIK 421
               P     RVD+G+E+GS + P+YD +++KLIV+ ++RE AI      L+   +  ++
Sbjct: 362 VLDFPV--NARVDTGVEAGSVISPFYDPMIAKLIVHSDTREEAIALLRSELSYLTVWPVR 419

Query: 422 TTIELYKWIMQDPDFQEGKFSTSYISQK 449
           T       ++ D DF   +  T  I ++
Sbjct: 420 TNAGFLFRLLGDGDFVRAQLDTGLIERR 447


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: 735
Number of extensions: 33
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 509
Length of database: 626
Length adjustment: 36
Effective length of query: 473
Effective length of database: 590
Effective search space:   279070
Effective search space used:   279070
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: 53 (25.0 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