GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Dyella japonica UNC79MFTsu3.2

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0484 N515DRAFT_0484
           glutaryl-CoA dehydrogenase
          Length = 389

 Score =  383 bits (984), Expect = e-111
 Identities = 196/376 (52%), Positives = 254/376 (67%), Gaps = 1/376 (0%)

Query: 18  SQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGS 77
           S LTD ERMV+D+   +  ER+LP + +AF   +  + +  E+  LGLLGAT+PEQYG +
Sbjct: 15  SLLTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLPEQYGCA 74

Query: 78  GMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGC 137
           GMN V YGLI +E+ER DSG RS  SVQSSL M PI  +G+EE K  YLPK+A GE +GC
Sbjct: 75  GMNGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAAGEIIGC 134

Query: 138 FGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAGDIRGFVL 197
           FGLTEP+ GSDP +M T ARK  G + ++GAKMWITN  +A + +VWA+ + G I+GF++
Sbjct: 135 FGLTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQTEDG-IQGFIV 193

Query: 198 EKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFTCLNSARYGIA 257
               +G +A  +H K+ LRAS+T  +  D V  PE N  P V+GLKGP  CL  ARYGI 
Sbjct: 194 PTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNVKGLKGPLGCLTQARYGIT 253

Query: 258 WGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLKD 317
           WG +GAA+AC +    YT +R  FGRPLA+NQ IQ KLA+M   IT+     L+LGRLKD
Sbjct: 254 WGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSLQLGRLKD 313

Query: 318 EGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTHD 377
            GN      S+ K N+C  ++DIAR  RD+LGG GI+ E    RH +NLE V TYEGT  
Sbjct: 314 AGNMQPTQVSLAKWNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESVITYEGTET 373

Query: 378 IHALILGRAITGLAAF 393
           +H L++GR +TG+ AF
Sbjct: 374 VHQLVVGRELTGINAF 389


Lambda     K      H
   0.319    0.136    0.409 

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: 392
Number of extensions: 13
Number of successful extensions: 2
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: 395
Length of database: 389
Length adjustment: 31
Effective length of query: 364
Effective length of database: 358
Effective search space:   130312
Effective search space used:   130312
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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 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