GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Methanoculleus horonobensis T10

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_067073807.1 MCUHO_RS04180 ATP-binding cassette domain-containing protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_001602375.1:WP_067073807.1
          Length = 277

 Score =  104 bits (260), Expect = 2e-27
 Identities = 74/230 (32%), Positives = 118/230 (51%), Gaps = 5/230 (2%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           LLE  ++   Y  +V  L+GVNF  E    + VIGPNGAGKSTL K   G+L P +G++ 
Sbjct: 3   LLETRSLTHIYRGNVHALEGVNFTAERKSRIAVIGPNGAGKSTLFKHFNGILKPTSGEVL 62

Query: 71  FKGKNIAGLKSNQIVR-LGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAM 129
            KG+ I      ++ + +G+ +      +F S +VE+++  G          +  ++   
Sbjct: 63  IKGEPITNANVREVRKFVGIVFQNPDDQIF-SPTVEQDVAFGPINLGLDETTVAHRVEEA 121

Query: 130 FPRL--SDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVK 187
              L   D R +    LSGGE++ +A+   L +EP +LVLDEP+A L P  VT +   V 
Sbjct: 122 LHLLGIEDLRERVPHHLSGGEKKRVAIAGILAMEPEVLVLDEPTAGLDPQGVTDLVRFVN 181

Query: 188 QINQE-GTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKV 236
           ++ +E G  ++    +     EMAD  YV++ G    SG   E+   P++
Sbjct: 182 RLPEEYGMTVVFSTHHLDLVAEMADYVYVMDRGTIVGSGTVGEVFARPEL 231


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: 173
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: 277
Length adjustment: 25
Effective length of query: 222
Effective length of database: 252
Effective search space:    55944
Effective search space used:    55944
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: 47 (22.7 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