GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Dyella japonica UNC79MFTsu3.2

Align Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized)
to candidate N515DRAFT_2297 N515DRAFT_2297 Cytochrome c, mono- and diheme variants

Query= SwissProt::O34215
         (441 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2297
          Length = 441

 Score =  247 bits (630), Expect = 6e-70
 Identities = 152/407 (37%), Positives = 216/407 (53%), Gaps = 34/407 (8%)

Query: 28  VKRGEYLARAGDCVACHSVKGGQPFAGGLPMATPIGTIYSTNITPDKTTGIGDYSYDDFQ 87
           V RGEYL RA DC ACH+V GGQP+ GG+    P GTIYSTNIT DK TGIGD+S D+F 
Sbjct: 53  VARGEYLTRAADCAACHTVPGGQPYTGGVAFKMPFGTIYSTNITADKETGIGDWSDDEFV 112

Query: 88  KAVRHGVAKNGDTLYPAMPYPSYAVVSDEDMKALYAYFMHGVAPVAQANKDSDIPWPLSM 147
           +A+  GV K+G  LYPA PY SY  +S +D+ A+ AY +  + P     + +++ +P   
Sbjct: 113 RALHAGVRKDGKPLYPAFPYTSYTALSRDDVLAIKAY-LFSLPPKHAPARPNELSFPFDQ 171

Query: 148 RWPLAIWRGVFAPDVKAFQPAAQEDPVLARGRYLVEGLGHCGACHTPRSITMQEKALSND 207
           RW L++W  +F    + ++P   +     RG YL   LGHC  CHTPR+     K     
Sbjct: 172 RWGLSVWNALFLKK-QRYEPVQGKSQAWNRGAYLATALGHCDECHTPRNAMYALK----- 225

Query: 208 GAHDYLSGSSAPIDGWTASNLRGDNRDGLGRWSEDDLRQFLRYGR-NDHTAAFGGMTDVV 266
              D LSG    + GW A N+  D   G+G WSE  L  +L  G  +    A G M +VV
Sbjct: 226 -RGDALSGE--VLQGWKAYNITSDKTYGIGNWSEQQLADYLSKGHASGRGTASGPMGEVV 282

Query: 267 EHSLQHLSDDDITAIARYLKSLGAKDASQTVFTQDDQVAKALWKGDDSQ---------TG 317
           ++SLQ+L+ +DI A+  YL+ +  +  S      +D+ A AL     +           G
Sbjct: 283 QYSLQYLTPEDIGALVTYLREVKPQQGS-AGSEVNDRPALALASSASAPGAEELAQGGLG 341

Query: 318 ASVYVDSCAACHKTDG----SRLSALLPGAAWQPGGAGEPDPTSLIHIVLTGGTLPGVQG 373
             ++  +C++CH  +G    S  +ALL   A     A +P   +L  ++L G TL    G
Sbjct: 342 QHLFQGACSSCHLWNGQGRQSEAAALLGTQA-----ANDPQAHNLTQVILQGSTLRTAHG 396

Query: 374 APTAITMPAFGWRLNDQQVADVVNFIRGSWGNGAKATVTAKDVASLR 420
                +MP+FG    D +VA + NF+   +G G  AT+TA +VA  R
Sbjct: 397 ---ETSMPSFGQAYTDAEVAALGNFVLTHFG-GKPATLTADEVAKRR 439


Lambda     K      H
   0.317    0.133    0.409 

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: 607
Number of extensions: 43
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 441
Length of database: 441
Length adjustment: 32
Effective length of query: 409
Effective length of database: 409
Effective search space:   167281
Effective search space used:   167281
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