GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Paraburkholderia bryophila 376MFSha3.1

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate H281DRAFT_04587 H281DRAFT_04587 hypothetical protein

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__Burk376:H281DRAFT_04587
          Length = 375

 Score =  274 bits (700), Expect = 3e-78
 Identities = 156/376 (41%), Positives = 215/376 (57%), Gaps = 11/376 (2%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           MDF  ++EQ+ L +++   L  +Y F++R+   +   G S   W  F E GL  LP  E 
Sbjct: 1   MDFTFNDEQQQLADALRRYLDRNYGFEARQAIVRSDAGISETHWAAFTELGLPALPVPEA 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSA-AQKAAHLPGIIDGSK 119
            GGF  GAV+ ++VM+ LG +LV+EPY  T V G   LR AG+   + A+ L     G  
Sbjct: 61  QGGFNGGAVDMLVVMQELGRALVVEPYWATAV-GVEALRLAGTGQGEDASLLERAAQGEI 119

Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179
             A A  E  +R+DL +++T A   G+   + G K VVL+G  A+  IV AR+ G     
Sbjct: 120 KLAVAFHEPKARYDLFEIATVATSQGEQHTLTGTKSVVLHGAQANYWIVPARSNGE---- 175

Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDD 239
             + +F+VP DA G+    Y T DG  AA + F G        +    +    +E + D 
Sbjct: 176 --IALFVVPRDAAGVKITDYRTIDGQRAATLEFNGTPA---RQLRGQHSGAAALEHIADY 230

Query: 240 ARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMF 299
               LCAEAVG +D   T TV+Y KTR+QFG PI  FQ LQHR  +M +  EQARS+   
Sbjct: 231 GTLLLCAEAVGALDALNTATVDYTKTRQQFGQPIARFQALQHRMVEMLIHAEQARSVTYL 290

Query: 300 ATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMI 359
           A M    +DA +R  AI+AAKV++G++ +FVGQQ++QLHGG+G+T E    H FKRL +I
Sbjct: 291 AAMRYSSEDADQRRRAISAAKVRVGQAARFVGQQAVQLHGGMGVTNEVAAAHLFKRLAII 350

Query: 360 EQTFGDTDHHLARVSA 375
           E T GD DHHLAR +A
Sbjct: 351 ETTLGDVDHHLARFAA 366


Lambda     K      H
   0.318    0.135    0.388 

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: 331
Number of extensions: 15
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: 380
Length of database: 375
Length adjustment: 30
Effective length of query: 350
Effective length of database: 345
Effective search space:   120750
Effective search space used:   120750
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: 50 (23.9 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