GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Paraburkholderia bryophila 376MFSha3.1

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate H281DRAFT_01762 H281DRAFT_01762 Cytochrome c, mono- and diheme variants

Query= metacyc::MONOMER-12746
         (434 letters)



>FitnessBrowser__Burk376:H281DRAFT_01762
          Length = 450

 Score =  359 bits (922), Expect = e-104
 Identities = 193/426 (45%), Positives = 263/426 (61%), Gaps = 16/426 (3%)

Query: 5   VIATLALLGSAAANAAEADQQ------ALVQQGEYLARAGDCVACHTA-KDGKPFAGGLP 57
           ++A L     A +++   D +      AL+ +G YLA+ GDC  CHT  K G PFAGGLP
Sbjct: 24  MVAALCAHSLAQSDSPSVDDEVSLSDPALISRGAYLAKLGDCAGCHTVPKQGAPFAGGLP 83

Query: 58  METPIGVIYSTNITPD-KTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDAD 116
           M +P G IYSTNITPD +TGIG YS+ DF++A+R GVA GG  LYPAMP+ S+ +++D+D
Sbjct: 84  MGSPFGTIYSTNITPDPQTGIGRYSYADFERALRDGVAPGGKRLYPAMPYASFTKINDSD 143

Query: 117 MQALYAYFMKGVAPVARDNQDSDIPWPLSMRWPLSIWRWMFAPSVETPAPAAGSDPVISR 176
           M ALYAYFM GV PVA    ++ +P+P S RW L+ W + F    E   P    D + +R
Sbjct: 144 MHALYAYFMHGVQPVAHRPPETKLPFPFSQRWGLAFWDFAFVQH-ERFIPDGKRDALWNR 202

Query: 177 GAYLVEGLGHCGACHTPRALTMQEKALSASGGSDFLSGSAPLEGWIAKSLRGDHKDGLGS 236
           GAY+V+ LGHCGACHTPR    +E+    S       G+   + W A +L GD   GLG 
Sbjct: 203 GAYIVQSLGHCGACHTPRGPGFEERGYDESSKLYLTGGTN--DHWFAPNLTGDPGSGLGR 260

Query: 237 WSEEQLVQFLKTGRSDRSAV--FGGMSDVVVHSMQYMTDADLTAIARYLKSLPANDPKD- 293
            S   +  FLK+G      V  FG M +VV  S QY +D DL A+ARYLKSLPA      
Sbjct: 261 LSPRDIASFLKSGHGVDVHVVTFGSMVEVVEDSGQYFSDDDLNAVARYLKSLPARQSSGA 320

Query: 294 -QPH-QYDKQVAQALWNGDDSKPGAAVYIDNCAACHRTDGHGYTRVFPALAGNPVLQSAD 351
            +P+ Q  ++ A +L  G+  +PGA +Y+  CA CH+ DG G    FPALAGNP + + D
Sbjct: 321 YKPNTQKLQETAVSLKAGEVERPGAGLYMSFCAKCHQADGRGEPHKFPALAGNPAVLAPD 380

Query: 352 ATSLIHIVLKGGTLPATHSAPSTFTMPAFAWRLSDQEVADVVNFIRSSWGNQASAVKPGD 411
            +SLI +VL+GGT P T + P    MPAF  + +D+E+A V++F+R++WGN+A  V   D
Sbjct: 381 TSSLIRLVLEGGTSPQTENGPIHREMPAFRNQFTDREIARVLSFVRTAWGNEARPVATRD 440

Query: 412 VAALRN 417
           V+ +R+
Sbjct: 441 VSTVRS 446


Lambda     K      H
   0.316    0.131    0.404 

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: 608
Number of extensions: 38
Number of successful extensions: 9
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: 434
Length of database: 450
Length adjustment: 32
Effective length of query: 402
Effective length of database: 418
Effective search space:   168036
Effective search space used:   168036
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: 51 (24.3 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