GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Shewanella oneidensis MR-1

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 200964 SO1802 peptide ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__MR1:200964
          Length = 335

 Score =  125 bits (313), Expect = 2e-33
 Identities = 89/310 (28%), Positives = 158/310 (50%), Gaps = 18/310 (5%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           LL   N+          V+A++ +S  +   E+ G+VGESG G++ L+  I + +  P  
Sbjct: 3   LLDVRNLTIELDTPHGKVRALEKVSLTLNAGEIHGLVGESGSGRSLLARAI-LGIPGPNW 61

Query: 65  LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIR-----MEKYV 119
            +     +      + +SS  R    R   G ++ +I Q    +L P+       M+   
Sbjct: 62  TITADRMMWDGNNLMAMSSKER----RNLMGSDMAMIFQDPSGSLDPSQTVGSQLMQAMP 117

Query: 120 RHLAESHGIDEEELLDKARRRFEEVGL-DPLWI-KRYPFELSGGMRQRAVIAIATILNPS 177
           ++         +     A++   +VG+ +P  +   Y +ELS G  Q+ +IA+A    P 
Sbjct: 118 KNPKAYFWQKHKHAKLTAQKWLHKVGIKNPQKVMSSYAWELSEGECQKVMIAMAIANQPR 177

Query: 178 LLIADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237
           LLIADEPT+++++  Q  + ++L Q+ +   V SI+ I+H++ T+ Q  D + ++Y G++
Sbjct: 178 LLIADEPTNSMELSTQAQIFRLLSQLNQLQNV-SILIISHELETLAQWCDHLSVLYCGQV 236

Query: 238 VEFAPVESLLEKPLHPYTQGLFNSVLTPE---PEVKKRGITTIPGAPPNLINPPSGCRFH 294
           +E  P + L+ +P HPYT+ L +++  P+    E  K  + T+PG+ P L + P GCR  
Sbjct: 237 MESGPTDELINQPYHPYTKALLDNM--PDYSGIEAHKAIMPTLPGSAPALQHLPIGCRLG 294

Query: 295 PRCPHAMDVC 304
           PRCP A   C
Sbjct: 295 PRCPEAQKKC 304


Lambda     K      H
   0.321    0.138    0.405 

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: 260
Number of extensions: 17
Number of successful extensions: 4
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: 330
Length of database: 335
Length adjustment: 28
Effective length of query: 302
Effective length of database: 307
Effective search space:    92714
Effective search space used:    92714
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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