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_RS10775 RR42_RS10775 alcohol dehydrogenase

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



>FitnessBrowser__Cup4G11:RR42_RS10775
          Length = 434

 Score =  362 bits (929), Expect = e-104
 Identities = 188/437 (43%), Positives = 250/437 (57%), Gaps = 30/437 (6%)

Query: 4   RRFARTAGWLAL---PCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLS 60
           RRF+ T  +  L   PC  AA                 +  GA    A V RG Y+A+++
Sbjct: 6   RRFSATVAFAVLLLAPCFAAAA----------------DAPGA----AQVERGRYLAKVA 45

Query: 61  DCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGG 120
           +C ACH+  G APFAGGL + T +G +++TNITPD  +GIG YS  +FDRA+R GVA  G
Sbjct: 46  NCAACHTSVGGAPFAGGLPLKTGVGTVYSTNITPDVDSGIGAYSFEEFDRALREGVARHG 105

Query: 121 RRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVF 180
           +RLYPAMPYPSY +L++ D++ALYA+    +K   Q     ++ WP  MRW + +WN +F
Sbjct: 106 KRLYPAMPYPSYARLAEPDVQALYAYLRTEVKAVRQATAEPEMRWPFGMRWLLRVWNWLF 165

Query: 181 APTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDG 240
             +    A   Q   WNRGAY+VQ   HCG+CHTPRG+   EK LDE    FLAGA ++G
Sbjct: 166 LESGPVPANAGQSVEWNRGAYLVQAVAHCGACHTPRGMLMAEKGLDERSRHFLAGASVEG 225

Query: 241 WYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA 300
           W + +LR DP TGLG WS   I ++L TGRNAHA  +G M+E   +STQFM   DL A+A
Sbjct: 226 WASTNLRGDPRTGLGTWSREDIAEYLHTGRNAHATSFGPMSEVIASSTQFMTRPDLDAVA 285

Query: 301 RYLKSLPGDPQRDGAPWQYQAVAAVQ------DAPGAHTYATRCASCHGLDGKGQPEWMP 354
            YLKS+PG  + D  P+ Y A  A        DA GA  YA  C  CHG +GKG     P
Sbjct: 286 VYLKSVPG-ARSDETPYAYDAHTADALAQGRFDATGARQYAEFCMPCHGANGKGFARVFP 344

Query: 355 PLAGATSALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRST 414
           PLAG  + +  + +S  N+ L+G+           Y MP +   L + E+A VL+++R+ 
Sbjct: 345 PLAGNPTVVDPDPSSLANLLLDGAVTAHVGTAATDYHMPGYGWTLDNQELANVLTFIRTG 404

Query: 415 WGNNGGAVDANAVGKLR 431
           WGN    V    V   R
Sbjct: 405 WGNQASQVKEATVAARR 421


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: 615
Number of extensions: 28
Number of successful extensions: 3
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: 434
Length adjustment: 32
Effective length of query: 415
Effective length of database: 402
Effective search space:   166830
Effective search space used:   166830
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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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