GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas litoralis 2SM5

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_090274985.1 BLU11_RS15705 isovaleryl-CoA dehydrogenase

Query= SwissProt::P81140
         (408 letters)



>NCBI__GCF_900105005.1:WP_090274985.1
          Length = 387

 Score =  172 bits (436), Expect = 2e-47
 Identities = 111/370 (30%), Positives = 190/370 (51%), Gaps = 9/370 (2%)

Query: 35  LIRDTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGVSSVAYG 93
           ++R+  + +    L PR    + + +F  ++  + G++G+LG T+ + YG AG+  +A+ 
Sbjct: 16  MLREQVQAFAAAELAPRAAAIDSDNLFPSDMWRKFGDMGLLGVTVSEEYGGAGLGYLAHV 75

Query: 94  LLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFGLTEPN 153
           +   E+ R  +    +    S+L ++ I   G+ EQ+  +YLP+L  GE +G   ++EPN
Sbjct: 76  VAMEEISRYSASVGLSYGAHSNLCVNQINRNGTAEQKT-RYLPKLISGEHIGALAMSEPN 134

Query: 154 HGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCE----DNCIRGFLLE 209
            GSD  SM+ RA  +     Y LNG+KTWITN P A+ +V++A+ +     + I  F++E
Sbjct: 135 AGSDVVSMKLRA--DKKGDRYILNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFIVE 192

Query: 210 KGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVLPKASS-LAVPFGCLNNARYGIS 268
           +  +G S      K  +R S T  +  DDVEVP EN+L   +  + V    L+  R  ++
Sbjct: 193 RDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPAENILGSENGGVKVLMSGLDYERAVLA 252

Query: 269 WGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACLQLGRLKD 328
            G  G  + CL     Y  DR QFG  + + Q IQ K+ADM T++         + +  D
Sbjct: 253 GGPTGIMQACLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYTVAQACD 312

Query: 329 QDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHD 388
           + + T +  + +       A  +A QA  +LGGNG  +E+   R   + +      GT +
Sbjct: 313 RGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFSTGRLLRDAKLYEIGAGTSE 372

Query: 389 IHALILGRAI 398
           I  +++GR +
Sbjct: 373 IRRMLIGREL 382


Lambda     K      H
   0.319    0.136    0.404 

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: 366
Number of extensions: 16
Number of successful extensions: 6
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: 408
Length of database: 387
Length adjustment: 31
Effective length of query: 377
Effective length of database: 356
Effective search space:   134212
Effective search space used:   134212
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.

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