GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Marinobacter adhaerens HP15

Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate GFF2711 HP15_2655 methylmalonate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-12387
         (496 letters)



>FitnessBrowser__Marino:GFF2711
          Length = 503

 Score =  199 bits (507), Expect = 1e-55
 Identities = 139/390 (35%), Positives = 195/390 (50%), Gaps = 11/390 (2%)

Query: 38  HPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLA 97
           +P TG     +     EDVD AV AA  AF  W  TP   R  ++ +F ELL  HK DLA
Sbjct: 27  NPATGQVTGRVALAGREDVDAAVAAADAAFPAWADTPPIRRARVMFKFLELLNTHKDDLA 86

Query: 98  DLVTIEAGKIRSEALGEVQEMIDICDFAVGLSRQLYGRTMPSERPGHRLMETWHPLGVVG 157
             +T E GK+ ++A GEV   IDI +FA G+ + L G        G     T  PLGVV 
Sbjct: 87  RAITAEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVA 146

Query: 158 VISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQ 217
            ++ FNFP  V  W   VA+  G+T V KPS   PL+ +A   + DL +  AG P G+  
Sbjct: 147 GVTPFNFPAMVPMWMFPVAIAAGNTFVLKPS---PLDPSASLMIADL-LKQAGLPDGVFN 202

Query: 218 VVVGAADVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGG-NNAAVVTPS 276
           VV G  D    L++ P V  +S  GST +   +  +  A+ G+ I  LGG  N  VV P 
Sbjct: 203 VVQGDKDAVNALIEHPDVQALSFVGSTPIANLLYEK-GAKHGKRIQALGGAKNHMVVMPD 261

Query: 277 ADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTL 336
           ADLD  V+A + AA G+AG+RC  +   ++  D+AD +V RL      L + +  Q    
Sbjct: 262 ADLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARSLKVKNGEQLDAE 321

Query: 337 VGPLVNEAAFGRMREAVERATAEGGTLCAGGE----RQFPDAAPGAYYVRPALV-RMPAQ 391
           +GP+V  AA  R+   +++  AEG  L   G         D     +++  +L   +   
Sbjct: 322 MGPIVTAAAHQRITGYIDKGVAEGAELVVDGRGFDASNTGDGCADGFWMGGSLFDHVTPD 381

Query: 392 TAVVREETFAPILYVLTYRDLDEAIRLNNE 421
             + REE F P+L  +   D+  AIRL N+
Sbjct: 382 MTIYREEIFGPVLACVRVPDIATAIRLIND 411


Lambda     K      H
   0.320    0.135    0.406 

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: 515
Number of extensions: 28
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: 496
Length of database: 503
Length adjustment: 34
Effective length of query: 462
Effective length of database: 469
Effective search space:   216678
Effective search space used:   216678
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: 52 (24.6 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:

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