GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Sphingobium czechense LL01

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_066599158.1 V473_RS00455 cell division ATP-binding protein FtsE

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_001046645.1:WP_066599158.1
          Length = 236

 Score =  102 bits (253), Expect = 1e-26
 Identities = 62/199 (31%), Positives = 104/199 (52%), Gaps = 7/199 (3%)

Query: 2   ARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGN 61
           A V  E++   Y G    T+ D +  +    F    G SG GKT+ L+++   +  + G 
Sbjct: 3   AIVQFENVGLRY-GLDSETLSDVSFSLAGGGFYFLTGASGAGKTSLLKLLYLAQRPSRGV 61

Query: 62  LYIGDRRVNDVPPKD-----RDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRV 116
           + +    V  +P K      R I +VFQ++ L PH++ Y N+A  L++  + + EID  V
Sbjct: 62  IRLFGEDVVTLPRKRLPGFRRRIGVVFQDFRLVPHLSAYDNIALPLRVSGMEEGEIDAPV 121

Query: 117 QEAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRA 176
            E    + +      +P  LSGG++QRVA+ RA++  P++ + DEP  N+DA +  ++  
Sbjct: 122 VEMLNWVGLGDRGQARPATLSGGEQQRVAIARAVIGRPEILVADEPTGNVDADMARRLMT 181

Query: 177 EIRKLHQRLQTTVIYVTHD 195
               L+ RL TT++  THD
Sbjct: 182 LFEALN-RLGTTIVVATHD 199


Lambda     K      H
   0.321    0.138    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: 221
Number of extensions: 10
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: 384
Length of database: 236
Length adjustment: 27
Effective length of query: 357
Effective length of database: 209
Effective search space:    74613
Effective search space used:    74613
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: 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