GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Methylocapsa aurea KYG

Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_036258213.1 DL86_RS03210 aldehyde dehydrogenase

Query= CharProtDB::CH_018413
         (862 letters)



>NCBI__GCF_000746085.1:WP_036258213.1
          Length = 477

 Score =  264 bits (674), Expect = 1e-74
 Identities = 161/448 (35%), Positives = 246/448 (54%), Gaps = 16/448 (3%)

Query: 8   ELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLVEDKVI 67
           E++  +   + AQ     Y+QE  D +          +R  LAK AV E G G V+DKV 
Sbjct: 20  EIEAMVGRARVAQAAIEHYAQEEADALVTAVGWQVYKSREALAKLAVEEGGFGNVQDKVA 79

Query: 68  KNHFAGEYI--YNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIFKSL 125
           K  FA   +         KTCG++E +   G+ KIA+P+GV+AA+IP T P +T   K+L
Sbjct: 80  K--FANRVMGTLTDMASIKTCGVVEEDPARGLIKIAKPVGVIAALIPTTGPDATPPVKAL 137

Query: 126 ISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLMQKA 185
            +LK RN I  +PHPR +K++    + +    ++ GAP ++I  I+ PSI  T+ LM+ +
Sbjct: 138 GALKARNAIIIAPHPRTRKTSAAVVEVMRKGCLQVGAPADLIQVIERPSIAKTELLMRMS 197

Query: 186 DITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGVICA 245
           D+ +ATGG  +VK+AYSSG PA GVG GN   ++DE+A +  A   I  +KT+D    C 
Sbjct: 198 DLIVATGGAGMVKAAYSSGTPAYGVGVGNAVHVVDETADLDDAAQMIANAKTFDYATSCL 257

Query: 246 SEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNP--KIVGQSAYTIA 303
           ++ SV    SIY  +K +  ERG ++    E  +++  ++  G   P  ++V +SA  IA
Sbjct: 258 ADNSVAAHSSIYEALKRKLVERGGHVCAPAEKARLQAAMWPKGEHIPSIEVVAKSAARIA 317

Query: 304 AMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYE-ADNFDDALKKAVTLINLGG 362
            +AGI++      L+ E   +GE  PF+ EKLS VLA+Y  +   D A+     + +  G
Sbjct: 318 ELAGIELAPDRTFLMVEEDGVGEAHPFSGEKLSVVLALYRYSGGIDGAVDLVNRITSYQG 377

Query: 363 LGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCGFW 422
            GHT GI++      D +   +   +T R  VN   ++GA G + N  +P + +L CG W
Sbjct: 378 AGHTCGIHSSR---DDHVRTLAFGTRTARVIVNQSLNEGA-GSVRN-GLPYTLSLSCGTW 432

Query: 423 GGNSVSENVGPKHLLNI----KTVAERR 446
           GGN  +ENV  +H +N+    + VA RR
Sbjct: 433 GGNITTENVNVRHFVNLTWVSRPVAPRR 460


Lambda     K      H
   0.317    0.134    0.378 

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: 838
Number of extensions: 35
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: 862
Length of database: 477
Length adjustment: 38
Effective length of query: 824
Effective length of database: 439
Effective search space:   361736
Effective search space used:   361736
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 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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