GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Streptococcus massiliensis 4401825

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 WP_018371450.1 BN415_RS05735 ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_000341525.1:WP_018371450.1
          Length = 241

 Score =  115 bits (288), Expect = 8e-31
 Identities = 76/247 (30%), Positives = 128/247 (51%), Gaps = 20/247 (8%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +LE++N+  GYI ++ +L+ ++F + SG+LV +IG NGAGKST    I GLLTP+ G+I 
Sbjct: 1   MLEIKNLTGGYI-NIPVLKNISFTIPSGQLVGLIGLNGAGKSTTINEIIGLLTPYQGEIR 59

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRN-------DSLQPLK 123
             G  +A   SN   ++G  Y+P+  +++  L + E+LE  A   +       +++QPL 
Sbjct: 60  IDGMTLAENPSNYRSKIG--YIPETPSLYEELPLREHLETVAMAYDLDVDSAIEAVQPLL 117

Query: 124 DKIFAMFPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVF 183
           +K      RL+D+        S G +Q + +  A ++ PSL ++DEP   L P+ +  + 
Sbjct: 118 EKF-----RLADKLDWFPVNFSKGMKQKVMIICAFLVNPSLFIVDEPFLGLDPVAIADLI 172

Query: 184 EQVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQEL-----LTDPKVAE 238
           E + +  + G +I++       A +M D   +L  G     G   EL     L    + E
Sbjct: 173 ELLDEEKKRGKSILMSTHVLDSAEKMCDSFVILHQGEIRAQGSLDELRSQFDLPTASLNE 232

Query: 239 LYLGAGK 245
           +YL   K
Sbjct: 233 IYLALTK 239


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: 147
Number of extensions: 7
Number of successful extensions: 2
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: 241
Length adjustment: 24
Effective length of query: 223
Effective length of database: 217
Effective search space:    48391
Effective search space used:    48391
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 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