GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adhBqn in Dyella japonica UNC79MFTsu3.2

Align Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized)
to candidate N515DRAFT_2297 N515DRAFT_2297 Cytochrome c, mono- and diheme variants

Query= SwissProt::P0A388
         (468 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2297
          Length = 441

 Score =  237 bits (604), Expect = 7e-67
 Identities = 144/415 (34%), Positives = 207/415 (49%), Gaps = 27/415 (6%)

Query: 21  ALAQTPDADSALVQKGAYVARLGDCVACHTALHGQSYAGGLEIKSPIGTIYSTNITPDPT 80
           A A  P + +  V +G Y+ R  DC ACHT   GQ Y GG+  K P GTIYSTNIT D  
Sbjct: 41  AAAGAPASLTDPVARGEYLTRAADCAACHTVPGGQPYTGGVAFKMPFGTIYSTNITADKE 100

Query: 81  YGIGRYTFAEFDEAVRHGIRKDGSTLYPAMPYPSFSRMTKEDMQALYAYFMHGVKPVAQP 140
            GIG ++  EF  A+  G+RKDG  LYPA PY S++ ++++D+ A+ AY +  + P   P
Sbjct: 101 TGIGDWSDDEFVRALHAGVRKDGKPLYPAFPYTSYTALSRDDVLAIKAY-LFSLPPKHAP 159

Query: 141 DKQPDISWPLSMRWPLGIWRMMFSPSPKDFTPAPGTDPEIARGDYLVTGPGHCGACHTPR 200
            +  ++S+P   RW L +W  +F    + + P  G      RG YL T  GHC  CHTPR
Sbjct: 160 ARPNELSFPFDQRWGLSVWNALFLKKQR-YEPVQGKSQAWNRGAYLATALGHCDECHTPR 218

Query: 201 GFAMQEKALDAAGGPDFLSGGAPIDNWVAPSLRNDPVVGLGRWSEDDIYTFLKSGRID-H 259
                  A+ A    D LSG   +  W A ++ +D   G+G WSE  +  +L  G     
Sbjct: 219 ------NAMYALKRGDALSGEV-LQGWKAYNITSDKTYGIGNWSEQQLADYLSKGHASGR 271

Query: 260 SAVFGGMGDVVAWSTQYFTDDDLHAIAKYLKSLPPVPPSQGNYTYDPSTANMLASGNTAS 319
               G MG+VV +S QY T +D+ A+  YL+    V P QG+   + +    LA  ++AS
Sbjct: 272 GTASGPMGEVVQYSLQYLTPEDIGALVTYLRE---VKPQQGSAGSEVNDRPALALASSAS 328

Query: 320 VPGADTYVK----------ECAICHRNDGGGVARMFPPLAGNPVVVTENPTSLVNVIAHG 369
            PGA+   +           C+ CH  +G G       L G          +L  VI  G
Sbjct: 329 APGAEELAQGGLGQHLFQGACSSCHLWNGQGRQSEAAALLGTQAANDPQAHNLTQVILQG 388

Query: 370 GVLPPSNWAPSAVAMPGYSKSLSAQQIADVVNFIRTSWGNKAPGTVTAADVTKLR 424
             L     A    +MP + ++ +  ++A + NF+ T +G K P T+TA +V K R
Sbjct: 389 STL---RTAHGETSMPSFGQAYTDAEVAALGNFVLTHFGGK-PATLTADEVAKRR 439


Lambda     K      H
   0.317    0.134    0.425 

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: 650
Number of extensions: 48
Number of successful extensions: 10
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: 468
Length of database: 441
Length adjustment: 33
Effective length of query: 435
Effective length of database: 408
Effective search space:   177480
Effective search space used:   177480
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