GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Algoriphagus aquaeductus T4

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase

Query= BRENDA::Q92947
         (438 letters)



>NCBI__GCF_003253485.1:WP_111393848.1
          Length = 401

 Score =  399 bits (1026), Expect = e-116
 Identities = 204/398 (51%), Positives = 278/398 (69%), Gaps = 4/398 (1%)

Query: 39  QLAKSSRPE-FDWQDPLVLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREII 97
           ++ KS + + F+  D L L++ LT ++ LIR + R + ++ + P I    +   F  EI+
Sbjct: 5   EIQKSLKQDLFEGVDFLDLDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIV 64

Query: 98  SEMGELGVLGPTIK-GYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYG 156
            + GE+G  GP +   YGC G+  ++YGL+ +E+ER DSG RS  SVQ SLVM+PIY +G
Sbjct: 65  KKFGEVGAFGPQLPVEYGCGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFG 124

Query: 157 SEEQRQKYLPQLAKGELLGCFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNS 216
           +EEQR KYLP+LA GELLGCFGLTEP+ GS+PS M T  ++      Y LNG K WI+NS
Sbjct: 125 TEEQRLKYLPRLASGELLGCFGLTEPDHGSNPSGMVT--NFKDMGDHYLLNGAKMWISNS 182

Query: 217 PMADLFVVWARCEDGCIRGFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENV 276
           P AD+ VVWA+ E+G I+G ++E+GM G S P    K+SLRAS TG ++ D V+VP+EN+
Sbjct: 183 PKADIAVVWAKNEEGRIQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENL 242

Query: 277 LPGASSLGGPFGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKL 336
           LPG + LG P  CL++AR+GIAWG +GA+  C  +AR+YA +R+QFG P+   QL QKKL
Sbjct: 243 LPGKTGLGAPMMCLDSARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKL 302

Query: 337 ADMLTEITLGLHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISD 396
           A+MLTEIT       ++G++ ++ KA    +S+ KRNN   AL+IAR+AR + GG GI+ 
Sbjct: 303 AEMLTEITKAQLLAWKVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITG 362

Query: 397 EYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 434
           EY ++RH MNLE+V TYEGTHDIH LILG  ITGIQAF
Sbjct: 363 EYPIMRHMMNLESVITYEGTHDIHLLILGNEITGIQAF 400


Lambda     K      H
   0.319    0.135    0.400 

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: 468
Number of extensions: 18
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: 438
Length of database: 401
Length adjustment: 32
Effective length of query: 406
Effective length of database: 369
Effective search space:   149814
Effective search space used:   149814
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 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