GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Shewanella oneidensis MR-1

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 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__MR1:200225
          Length = 241

 Score =  115 bits (288), Expect = 8e-31
 Identities = 74/233 (31%), Positives = 127/233 (54%), Gaps = 9/233 (3%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           ++ + N+H  Y  D  +L+G+N  +  GE+V+VIGP+G+GKST  + I  L  P  G I 
Sbjct: 1   MINITNLHKSY-GDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIE 59

Query: 71  FKGKNIAGLKS---NQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKD-KI 126
            +G++I    +       ++GM +  Q  N+FP  +V +N+ +         Q   D K 
Sbjct: 60  IEGQSITAKDACVDKLRQKVGMVF--QNFNLFPHKTVLQNITLAPVSLKLMTQAEADNKA 117

Query: 127 FAMFPR--LSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFE 184
            A+  +  L D+      +LSGG++Q +A+ +AL +EP L++ DEP++AL P +V  V +
Sbjct: 118 LALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDVLD 177

Query: 185 QVKQINQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVA 237
            +K + Q+G  +++V      A +++DR   ++ G    S   +EL T PK A
Sbjct: 178 VMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEA 230


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: 144
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 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