GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS10775 RR42_RS10775 alcohol
           dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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