Alignments for a candidate for drdehyd-cytc in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for drdehyd-cytc in Dyella japonica UNC79MFTsu3.2

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate N515DRAFT_2297 N515DRAFT_2297 Cytochrome c, mono- and diheme variants

Query= reanno::WCS417:GFF2133
         (447 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2297
          Length = 441

 Score =  245 bits (625), Expect = 2e-69
 Identities = 145/443 (32%), Positives = 221/443 (49%), Gaps = 35/443 (7%)

Query: 13  LALPCLVAAGLLA-----WYVTREPATPFEQEQAGATFEPAL---VSRGEYVARLSDCVA 64
           LAL  +V  G  A     W++  +       + A A    +L   V+RGEY+ R +DC A
Sbjct: 8   LALIAIVVVGAAAFTAYAWFIVGDGKETGAPQPAAAGAPASLTDPVARGEYLTRAADCAA 67

Query: 65  CHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRRLY 124
           CH++ G  P+ GG+    P G I++TNIT DK TGIG +S  +F RA+  GV   G+ LY
Sbjct: 68  CHTVPGGQPYTGGVAFKMPFGTIYSTNITADKETGIGDWSDDEFVRALHAGVRKDGKPLY 127

Query: 125 PAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAPTA 184
           PA PY SY  LS DD+ A+ A+    + P + P  P+++ +P + RW +++WN +F    
Sbjct: 128 PAFPYTSYTALSRDDVLAIKAYLF-SLPPKHAPARPNELSFPFDQRWGLSVWNALFLKKQ 186

Query: 185 TYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWYAP 244
            Y     +   WNRGAY+    GHC  CHTPR   +  K  D      L+G +L GW A 
Sbjct: 187 RYEPVQGKSQAWNRGAYLATALGHCDECHTPRNAMYALKRGDA-----LSGEVLQGWKAY 241

Query: 245 SLRQDPNTGLGRWSEPQIVQFLKTGR-NAHAVVYGSMTEAFNNSTQFMQDDDLAAIARYL 303
           ++  D   G+G WSE Q+  +L  G  +      G M E    S Q++  +D+ A+  YL
Sbjct: 242 NITSDKTYGIGNWSEQQLADYLSKGHASGRGTASGPMGEVVQYSLQYLTPEDIGALVTYL 301

Query: 304 KSLPGDPQRDGAPWQYQ-----AVAAVQDAPGA----------HTYATRCASCHGLDGKG 348
           + +   PQ+  A  +       A+A+   APGA          H +   C+SCH  +G+G
Sbjct: 302 REV--KPQQGSAGSEVNDRPALALASSASAPGAEELAQGGLGQHLFQGACSSCHLWNGQG 359

Query: 349 QPEWMPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVL 408
           +      L G  +A   ++ +   + L GS    A G      MP+F +  +D E+A + 
Sbjct: 360 RQSEAAALLGTQAANDPQAHNLTQVILQGSTLRTAHGETS---MPSFGQAYTDAEVAALG 416

Query: 409 SYVRSTWGNNGGAVDANAVGKLR 431
           ++V + +G     + A+ V K R
Sbjct: 417 NFVLTHFGGKPATLTADEVAKRR 439


Lambda     K      H
   0.318    0.133    0.423 

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: 630
Number of extensions: 46
Number of successful extensions: 8
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: 447
Length of database: 441
Length adjustment: 32
Effective length of query: 415
Effective length of database: 409
Effective search space:   169735
Effective search space used:   169735
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: 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources