GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-cytc in Cronobacter condimenti 1330

Align cytochrome c component of deoxyribose dehydrogenase (characterized)
to candidate WP_007665341.1 BN137_RS16385 c-type cytochrome

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



>NCBI__GCF_000319285.1:WP_007665341.1
          Length = 398

 Score =  358 bits (920), Expect = e-103
 Identities = 185/384 (48%), Positives = 244/384 (63%), Gaps = 14/384 (3%)

Query: 50  VSRGEYVARLSDCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFD 109
           +SRGEYVAR  DC+ACH+ A  AP AGG++ ATPLG I++TNITPD + GIG YS  DF 
Sbjct: 21  MSRGEYVARAGDCMACHTAADGAPLAGGVKFATPLGDIYSTNITPDNTHGIGGYSYEDFA 80

Query: 110 RAVRHGVAPGGRRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNM 169
           RA+R GVA  G  LYPAMPYPSY K+SD+D++ALY + M  +KP    N  SDIPWPL+M
Sbjct: 81  RAMREGVAKDGHHLYPAMPYPSYAKMSDEDLRALYEYLMNEVKPQATANRDSDIPWPLSM 140

Query: 170 RWPIALWNGVFAPTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAG 229
           RWP+ +WN +FA    +  + D+ A WNRGAY+VQGPGHCG+CHTPRG+   EKA DE  
Sbjct: 141 RWPLGIWNSLFADEKPFTPRADKSAQWNRGAYLVQGPGHCGACHTPRGIGMQEKAFDERD 200

Query: 230 APFLAGALLDGWYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQ 289
             FLAG  L+GWYAPSLR     GL + SE  +   L+ GR+ HA + G M E   NSTQ
Sbjct: 201 EQFLAGEELNGWYAPSLR-----GL-KMSEGDLTLLLRDGRSKHAALSGPMDEVVTNSTQ 254

Query: 290 FMQDDDLAAIARYLKSLPG-DPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKG 348
           ++ DDD  AIA YL SLPG +P +  AP  + + AA+++  G   YA  CA+CH  +G+G
Sbjct: 255 YLSDDDNRAIASYLLSLPGSEPVKTQAP--HLSQAALEN--GHQLYARYCATCHASNGEG 310

Query: 349 QPEWMPPLAGATSALAKESASAINITLNGSQRVVAS-GVPDAYRMPAFREQLSDTEIAEV 407
               +P L    +  A    + + + L G +  V    +P  Y MP +   LSD + A+V
Sbjct: 311 ADYAVPALKDNLTVNADNPLTLLRVVLEGGKTAVTERHLP--YSMPGYGWALSDQDAADV 368

Query: 408 LSYVRSTWGNNGGAVDANAVGKLR 431
            +Y+R ++GN+   V  + V   R
Sbjct: 369 TNYIRGSFGNHAAPVTPDQVKDAR 392


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: 600
Number of extensions: 22
Number of successful extensions: 4
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: 398
Length adjustment: 32
Effective length of query: 415
Effective length of database: 366
Effective search space:   151890
Effective search space used:   151890
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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