GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Herbaspirillum seropedicae SmR1

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 HSERO_RS06785 HSERO_RS06785 metal-dependent hydrolase

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__HerbieS:HSERO_RS06785
          Length = 249

 Score =  208 bits (530), Expect = 7e-59
 Identities = 111/241 (46%), Positives = 162/241 (67%), Gaps = 6/241 (2%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +LEV ++ A Y K V++L G++  VE G++VTVIGPNGAGK+TL   I G+L P  G + 
Sbjct: 5   VLEVRDLSAAYGK-VEVLAGIDLSVEQGKIVTVIGPNGAGKTTLLSAIMGVL-PSRGAMA 62

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQ----PLKDKI 126
           F G      +  ++V  GM  VP+   +F  +++E+NL +GAF R  + Q       +++
Sbjct: 63  FDGAIRHSPEVEEMVAAGMTLVPEKRELFAEMNIEDNLMLGAFQRYRTGQRDHAATLEEV 122

Query: 127 FAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQV 186
           + +FPRL +RR Q+AGTLSGGERQMLA+G+ALM +P LL+LDEPS  L+P++V ++F  +
Sbjct: 123 YTLFPRLRERRSQQAGTLSGGERQMLAVGRALMAKPRLLMLDEPSLGLAPLIVREIFRII 182

Query: 187 KQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLGAGKG 246
            ++ + G +I+LVEQNAR AL++AD GYVLE+G   + GP  +L  D +V E YLG    
Sbjct: 183 AELRRRGVSILLVEQNARAALQVADYGYVLENGAIRMHGPASQLAHDRRVIEAYLGLSGK 242

Query: 247 H 247
           H
Sbjct: 243 H 243


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: 188
Number of extensions: 8
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: 249
Length adjustment: 24
Effective length of query: 223
Effective length of database: 225
Effective search space:    50175
Effective search space used:    50175
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