GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manZ in Weissella oryzae SG25

Align PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized)
to candidate WP_045477156.1 TT13_RS09605 PTS mannose/fructose/sorbose transporter family subunit IID

Query= SwissProt::P69805
         (283 letters)



>NCBI__GCF_000691805.2:WP_045477156.1
          Length = 324

 Score =  277 bits (709), Expect = 2e-79
 Identities = 144/322 (44%), Positives = 208/322 (64%), Gaps = 45/322 (13%)

Query: 5   TQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQA 64
           T TT +  L++     V + S   QGSWN+ERMQ +G+ FS++PA++RLY    E  K A
Sbjct: 3   TNTTKKVTLSKGTRFKVMMSSMFIQGSWNYERMQNVGWAFSLMPALKRLYKPGTEEAKLA 62

Query: 65  IRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFW 124
           ++RH+EFFNT P++A+PILGVTLALEE+RANGA+ID+ AI G+KVG+MGPLAG+GDP+FW
Sbjct: 63  LQRHMEFFNTHPYLASPILGVTLALEEERANGAKIDNAAIQGVKVGMMGPLAGIGDPVFW 122

Query: 125 GTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGF 184
            TVRP+  A+ A +A+SGS++ P++FF+ +N++R+A  +Y   +GY +G  I  D+GGG 
Sbjct: 123 FTVRPIIGAIAASLAVSGSIIAPIVFFVAWNIIRIAFLWYTQEFGYKQGTAITGDLGGGM 182

Query: 185 LQKLTEGASILGLFVMGALVNKWTHVN----------IPL-----------------VVS 217
           LQK+T+GASILG+FV+GAL+ +W  ++          +PL                 + +
Sbjct: 183 LQKVTKGASILGMFVLGALIQRWVSISWTGPNSVVSKLPLSKGAYLDWNSLPSGAQGIKT 242

Query: 218 RIT-----DQTGK----------EHVTTVQTILDQLMPGLVPLLLTFACMWLLRK---KV 259
            IT     D +G             +T +Q  L+ L+PGL  LLLTF  +WLLRK   + 
Sbjct: 243 AITTLFKQDASGNLTQSGVYMTPNKITYLQDNLNMLLPGLSALLLTFLVIWLLRKFKSRN 302

Query: 260 NPLWIIVGFFVIGIAGYACGLL 281
            PL+II+G F+ GI  +  GL+
Sbjct: 303 TPLYIIIGLFIFGILLHWAGLM 324


Lambda     K      H
   0.326    0.143    0.439 

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: 279
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 283
Length of database: 324
Length adjustment: 27
Effective length of query: 256
Effective length of database: 297
Effective search space:    76032
Effective search space used:    76032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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