GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh2 in Echinicola vietnamensis KMM 6221, DSM 17526

Align D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized)
to candidate Echvi_1808 Echvi_1808 Cytochrome c.

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



>FitnessBrowser__Cola:Echvi_1808
          Length = 330

 Score = 87.8 bits (216), Expect = 4e-22
 Identities = 89/294 (30%), Positives = 134/294 (45%), Gaps = 55/294 (18%)

Query: 28  VQQGEYLAR-AGDCVACHTAKDGKPFAG------------------GLPMETPIGVIYST 68
           + +GEYLA     C+ CH+ ++   F+G                  GLP     GV  S 
Sbjct: 48  IARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRFDRSMGLP-----GVFVSP 102

Query: 69  NITPDKTGIGDYSFEDFDKAVRHGVAKGGSTLYPAMPFPSYARVSDADMQALYAYFMKGV 128
           NITP+  GIG+++  +  + +  GV K G  ++P MP+ SY ++   D++A+ AY ++ +
Sbjct: 103 NITPE--GIGNWTDGELYRLITTGVKKNGEPIFPVMPYQSYGKLDPEDIKAVIAY-IRTL 159

Query: 129 APVARDNQDSDIPWPLSMRWPLS-IWRWMFAPSVETPAPAAGSDPVISRGAYLVEGLGHC 187
           AP     Q S+IP P  + +P++ I R M  PS  TP      + VI+ G YLV     C
Sbjct: 160 AP-----QKSNIP-PREIDFPVNFIIRTM--PSKATPTTRPNKEDVIAYGEYLVTAAA-C 210

Query: 188 GACHTPRALTMQEKALSASGGSDFLSGS----APLEGWIAKSLRGDHKDGLGSWSEEQLV 243
           G CHT        K         +L G     +P    +  S    H  GLG+ S+E  V
Sbjct: 211 GECHT--------KFEKGKFVGPYLGGGRAFPSPNGNIVRSSNLTFHSTGLGNKSKEDFV 262

Query: 244 QFLKTGRSD---RSAVFGGMSDVVVHSMQY--MTDADLTAIARYLKSL-PANDP 291
           +  K    +    + V  G    ++    Y  M   DL +I  YL+SL P N+P
Sbjct: 263 RQFKQYSPELYTPTKVGEGEFQTIMPWTMYAGMDTTDLASIYEYLRSLEPINNP 316



 Score = 52.0 bits (123), Expect = 3e-11
 Identities = 35/131 (26%), Positives = 59/131 (45%), Gaps = 14/131 (10%)

Query: 14  SAAANAAEADQQALVQQGEYLARAGDCVACHTAKD-----GKPFAGGLPMETPIG-VIYS 67
           S A      +++ ++  GEYL  A  C  CHT  +     G    GG    +P G ++ S
Sbjct: 184 SKATPTTRPNKEDVIAYGEYLVTAAACGECHTKFEKGKFVGPYLGGGRAFPSPNGNIVRS 243

Query: 68  TNITPDKTGIGDYSFEDFDKAVRH-------GVAKGGSTLYPAMPFPSYARVSDADMQAL 120
           +N+T   TG+G+ S EDF +  +            G       MP+  YA +   D+ ++
Sbjct: 244 SNLTFHSTGLGNKSKEDFVRQFKQYSPELYTPTKVGEGEFQTIMPWTMYAGMDTTDLASI 303

Query: 121 YAYFMKGVAPV 131
           Y Y ++ + P+
Sbjct: 304 YEY-LRSLEPI 313



 Score = 36.2 bits (82), Expect = 2e-06
 Identities = 32/137 (23%), Positives = 60/137 (43%), Gaps = 13/137 (9%)

Query: 169 GSDPVISRGAYLVEGLGHCGACHTPRALTM----QEKALSASGGSDFLSGSAPLEG-WIA 223
           GS   I+RG YL   +  C  CH+ R  ++            GG  F   S  L G +++
Sbjct: 43  GSTEQIARGEYLANHVMLCMDCHSDRNYSLFSGPPHPGTKGLGGDRF-DRSMGLPGVFVS 101

Query: 224 KSLRGDHKDGLGSWSEEQLVQFLKTG-RSDRSAVFGGMSDVVVHSMQYMTDADLTAIARY 282
            ++     +G+G+W++ +L + + TG + +   +F  M      S   +   D+ A+  Y
Sbjct: 102 PNIT---PEGIGNWTDGELYRLITTGVKKNGEPIFPVMP---YQSYGKLDPEDIKAVIAY 155

Query: 283 LKSLPANDPKDQPHQYD 299
           +++L        P + D
Sbjct: 156 IRTLAPQKSNIPPREID 172


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: 383
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 434
Length of database: 330
Length adjustment: 30
Effective length of query: 404
Effective length of database: 300
Effective search space:   121200
Effective search space used:   121200
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: 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