GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Halomonas xinjiangensis TRM 0175

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043529919.1 JH15_RS10235 SDR family oxidoreductase

Query= BRENDA::A0A075B5H4
         (258 letters)



>NCBI__GCF_000759345.1:WP_043529919.1
          Length = 254

 Score =  213 bits (543), Expect = 2e-60
 Identities = 107/259 (41%), Positives = 163/259 (62%), Gaps = 6/259 (2%)

Query: 1   MFSDLKGKRILITGSTEGIGMATAIELARYGAVVGLNSHVDPADPALLLGKLREAGGDGA 60
           MF +L+GKR+LITG++ GIG A A  +   GA V ++ H        +  ++  AGG   
Sbjct: 1   MFDELRGKRVLITGASRGIGAAVAKRMGALGAHVAVHYHSSEGPAKAVCEEIEAAGGKAV 60

Query: 61  FFRADITKTAECQRLVSAFVERFDGIDVLINNAGGLAGRSNLENIDDAFYDRVMDLNGRS 120
             + D+++++E  R+V    +   G+D+L+NNAG + GR +L +IDD  YDRV+DLN RS
Sbjct: 61  CLKGDVSRSSEAVRVVEEAAKALGGLDILVNNAGDMLGRVSLADIDDDHYDRVLDLNVRS 120

Query: 121 VLMMTKFAIPHLRASAKASGTTSAVISTGSIAAREGGGIGAGVYAASKAWLHDIHRNWVK 180
           V+  ++ A+P+ R   + +     +I T SIAAR GGG GAG+YA++K ++  + RN  K
Sbjct: 121 VIAASRAALPYFRQQGRGN-----IIHTSSIAARNGGGPGAGLYASAKGFVSTLTRNMAK 175

Query: 181 EFTKDSIRFNIVAPGTVDTAFHADKSDELKTRIAN-SIPMGRFGTVQELAPAYVFFASHA 239
           E   D+IR N VAPGT+ T FH   S++ +   A  +IP GR G+ ++   AY+F A+ A
Sbjct: 176 ELAGDNIRVNAVAPGTIATDFHERHSNDAQLEAARATIPQGRLGSAEDCVGAYLFLATDA 235

Query: 240 ASGYITGQILDVNGGQICP 258
            S Y+TGQ+++VNGGQ+ P
Sbjct: 236 LSDYVTGQVIEVNGGQLMP 254


Lambda     K      H
   0.320    0.136    0.397 

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: 165
Number of extensions: 6
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: 258
Length of database: 254
Length adjustment: 24
Effective length of query: 234
Effective length of database: 230
Effective search space:    53820
Effective search space used:    53820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 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