GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_0484
          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.

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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