GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Pedobacter sp. GW460-11-11-14-LB5

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__Pedo557:CA265_RS04345
          Length = 216

 Score =  125 bits (315), Expect = 7e-34
 Identities = 70/215 (32%), Positives = 113/215 (52%), Gaps = 7/215 (3%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           L+ T + KS+G +++LK +N  V+ GE V  +GPSG GKSTLL ++  L+    G + + 
Sbjct: 2   LKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQLK 61

Query: 64  GQTVTT------TPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEA 117
           G  +        +    + I  VFQ + L P  S  EN+ +     +  K++   R  E 
Sbjct: 62  GTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFEL 121

Query: 118 SRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIA 177
             +  L+D    +P++LSGG++QRVAI RA++  P + L DEP  NLD+           
Sbjct: 122 LDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQLFV 181

Query: 178 RLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRI 212
            L      + + VTH++  A T +D++V ++DG I
Sbjct: 182 SLRDNFHQTFVIVTHNEHLAKT-SDRVVSMKDGLI 215


Lambda     K      H
   0.320    0.137    0.391 

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: 137
Number of extensions: 6
Number of successful extensions: 2
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: 331
Length of database: 216
Length adjustment: 25
Effective length of query: 306
Effective length of database: 191
Effective search space:    58446
Effective search space used:    58446
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: 47 (22.7 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