GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Pedobacter sp. GW460-11-11-14-LB5

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Pedo557:CA265_RS07485
          Length = 252

 Score =  151 bits (381), Expect = 2e-41
 Identities = 86/218 (39%), Positives = 129/218 (59%), Gaps = 3/218 (1%)

Query: 1   MIEFHDVHKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGG 60
           +I   ++ + Y +    I AL+   L+I  G+   L+G SG+GKSTL+ ++  L+ PS G
Sbjct: 5   LITIKEIGRKYVIGSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSG 64

Query: 61  RILVEGEDVTALDAEGLRRFR-QRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVD 119
             ++ G +V+ +  + L   R Q +G +FQ FNLL   T  DN+A+PL  AG  S+ + D
Sbjct: 65  TYVLNGTNVSHMSDDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGT-SKKDRD 123

Query: 120 ARVSELLARVGLSDHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTAS 179
           AR +  L  VGL +     P +LSGGQ+QRV +ARAL   PSI+L DE T  LD +T+  
Sbjct: 124 ARAARALENVGLGNRMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIE 183

Query: 180 VLQLLAEINRELKLTIVLITHEMDVIRRVCDQVAVMDG 217
           ++ LL EI+ +   TI+L+THE D+ +     V + DG
Sbjct: 184 IMGLLEEIHSKGN-TIILVTHEEDIAQHAHRIVRMRDG 220


Lambda     K      H
   0.322    0.138    0.393 

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: 180
Number of extensions: 7
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: 335
Length of database: 252
Length adjustment: 26
Effective length of query: 309
Effective length of database: 226
Effective search space:    69834
Effective search space used:    69834
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: 48 (23.1 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