GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Corynebacterium deserti GIMN1.010

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_082353390.1 CDES_RS05835 sugar ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>NCBI__GCF_001277995.1:WP_082353390.1
          Length = 523

 Score =  158 bits (399), Expect = 3e-43
 Identities = 89/241 (36%), Positives = 143/241 (59%), Gaps = 6/241 (2%)

Query: 6   PLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDIL 65
           P++++  + K FG V  +  VS+DV PG    LLG+NGAGKST IK MSGV++P  G IL
Sbjct: 14  PVLQLDRVSKSFGPVNVINQVSIDVRPGRVLALLGENGAGKSTLIKMMSGVYQPDGGQIL 73

Query: 66  FEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYAN 125
            +G+P    D + A A GIAT+HQ L ++P M+V+ N  +G  P RK G   + +  +  
Sbjct: 74  VDGKPTELPDTKAAEALGIATIHQELNLVPTMTVAENVMLGRTP-RKFG---MVNFKHLR 129

Query: 126 RITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTA 185
           R     +  +G+++   +  VG+L    +Q V IA+A+   A++LILDEPT+AL  R+  
Sbjct: 130 RQAQAALDLIGVDV-DLNAEVGSLGIARQQMVEIAKALSMNARILILDEPTAALTGREVD 188

Query: 186 NVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDMMA 245
            +   +D+++ +GVA+VFI+H++     +G+  +VL  G+ +      +   +EL  +M 
Sbjct: 189 QLFKVVDELKAKGVAMVFISHHLDEIARIGNTVSVLRDGQFIAELP-ANTDEDELVRLMV 247

Query: 246 G 246
           G
Sbjct: 248 G 248



 Score = 82.8 bits (203), Expect = 1e-20
 Identities = 59/229 (25%), Positives = 108/229 (47%), Gaps = 9/229 (3%)

Query: 3   MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62
           + +PL+ +    K+  +    + VS+ V  GE   L G  GAG++  +++++GV +   G
Sbjct: 262 LGKPLLEV----KNLSAAGRFSNVSLTVRAGEVVGLAGLVGAGRTEVVRSIAGVDRVDSG 317

Query: 63  DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLM---SVSRNFFMGNEPIRKIGPLKLF 119
           +++  G+ L   D  +AI  GI  + +      L+   SV  N  +G   +       L 
Sbjct: 318 EVIVAGKKLRGGDISEAIKNGIGHIPEDRKAQGLVLGSSVEDN--LGLATLASTAKAGLV 375

Query: 120 DHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSAL 179
           D    +    +  +K+ I +    Q +  LSGG +Q     R V  G+ VL+LDEPT  +
Sbjct: 376 DRKGQHERAADVAKKLRIRMANIKQPIKDLSGGNQQKAVFGRWVLAGSNVLLLDEPTRGV 435

Query: 180 GVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLG 228
            V     +   I+++  +G AV+ ++  +   L + DR  V++ G+  G
Sbjct: 436 DVGAKVEIYNIINEITARGGAVLMVSSELPEVLGMADRILVMSGGRIAG 484


Lambda     K      H
   0.321    0.137    0.395 

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: 343
Number of extensions: 18
Number of successful extensions: 4
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: 261
Length of database: 523
Length adjustment: 30
Effective length of query: 231
Effective length of database: 493
Effective search space:   113883
Effective search space used:   113883
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 (21.9 bits)
S2: 49 (23.5 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