GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Cupriavidus basilensis 4G11

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate RR42_RS20235 RR42_RS20235 metal-dependent hydrolase

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__Cup4G11:RR42_RS20235
          Length = 247

 Score =  221 bits (562), Expect = 1e-62
 Identities = 115/242 (47%), Positives = 164/242 (67%), Gaps = 8/242 (3%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLT---PHTG 67
           +LEV+++H  Y K V+ + G N +VE+G++VTVIGPNGAGKST+   I G L      TG
Sbjct: 4   ILEVKDLHVRYGK-VEAVHGANLKVEAGKIVTVIGPNGAGKSTMLNAIMGALPVSGSSTG 62

Query: 68  KITFKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRN----DSLQPLK 123
            +T+ G ++AGL +   V  GMC VP+   +F S+SV +NL +GA+ R      +     
Sbjct: 63  AVTYLGHDLAGLPAEGRVARGMCLVPEKRELFGSMSVADNLVLGAYRRKRAGEKNFLDQM 122

Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183
           + ++ +FPRL +R +Q AGTLSGGERQMLA+G+ALM +P LL+LDEPS  L+P++V ++F
Sbjct: 123 EVVYGLFPRLKERAKQDAGTLSGGERQMLAVGRALMAKPQLLMLDEPSLGLAPLIVKEIF 182

Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGA 243
             +  + + G A +L+EQNAR AL++AD GYV+E+G  A+ GP  EL  +PKV E YLG 
Sbjct: 183 HIINDLRKTGVATLLIEQNARAALQVADYGYVIETGDMAMEGPAGELAANPKVIETYLGL 242

Query: 244 GK 245
            K
Sbjct: 243 AK 244


Lambda     K      H
   0.317    0.136    0.377 

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: 198
Number of extensions: 9
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: 247
Length of database: 247
Length adjustment: 24
Effective length of query: 223
Effective length of database: 223
Effective search space:    49729
Effective search space used:    49729
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 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