GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Cupriavidus basilensis 4G11

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate RR42_RS21615 RR42_RS21615 alcohol dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS21615
          Length = 1000

 Score =  235 bits (600), Expect = 4e-66
 Identities = 150/431 (34%), Positives = 210/431 (48%), Gaps = 22/431 (5%)

Query: 4   RRFARTAGWLALPCLVAAGLLAWYVT-REPATPFEQEQAGATFEPALVSRGEYVARLSDC 62
           R  AR   WL      AAGL    +  R P  P     AG  +  A + RG  VA   DC
Sbjct: 558 RGAARKRNWLLAGATAAAGLFVTAMPWRAPIAPVAPPGAGF-YSAATIERGRLVAAAGDC 616

Query: 63  VACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGGRR 122
             CH+    A  AGGL + TP G I++TNITPD  TGIG +S A F+RA+R G+   GR 
Sbjct: 617 AVCHTAPNGARNAGGLALDTPFGTIYSTNITPDVETGIGNWSYAAFERAMRQGIHRDGRH 676

Query: 123 LYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVFAP 182
           LYPA PY ++ K SD D++ALYA+ M   +P       + + +P N+R  +A WN +F  
Sbjct: 677 LYPAFPYTAFAKTSDGDLQALYAYLM-AAEPVRAKAPETALAFPYNLRPLMAGWNLLFHS 735

Query: 183 TATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDGWY 242
              + A P + A WNRGAY+ +G GHC +CH+PR    N    ++ G  +L G   +GW 
Sbjct: 736 PKPFEADPARSAQWNRGAYLAEGLGHCSACHSPR----NALGAEQGGRRYLGGGEAEGWE 791

Query: 243 APSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIARY 302
           AP+L +  +  +  W+E  +  +L+TG   H                 + ++D+ AIA Y
Sbjct: 792 APALGKLSHAPV-PWTEQALFSYLRTGYAPHHGAAAGPMAPVIEELALLPEEDVRAIAHY 850

Query: 303 LKSLPGDPQRDGAPWQYQA---------VAAVQDAPGAHTYATRCASCHGLD-GKGQPEW 352
           + S  GD Q D A    QA          A     P A  Y   CA CH  D G  Q   
Sbjct: 851 VASF-GDAQPDAALASAQARQLEQRSADAARTLGGPAARLYQNACAVCHQSDQGIRQFGI 909

Query: 353 MPPLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVR 412
            P LA  T+    +  + I + L+G   +   G  D   MPAF E L D ++ +++ Y+R
Sbjct: 910 KPSLALNTNLHGDKPDNLIRVLLDG---IPTPGTSDLGYMPAFGESLDDRQLTQLVHYLR 966

Query: 413 STWGNNGGAVD 423
             +  +  A D
Sbjct: 967 KRFAPDKPAWD 977


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: 1376
Number of extensions: 77
Number of successful extensions: 6
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: 1000
Length adjustment: 38
Effective length of query: 409
Effective length of database: 962
Effective search space:   393458
Effective search space used:   393458
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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