GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Dinoroseobacter shibae DFL-12

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)

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



>FitnessBrowser__Dino:3607124
          Length = 338

 Score =  347 bits (890), Expect = e-100
 Identities = 184/338 (54%), Positives = 235/338 (69%), Gaps = 7/338 (2%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  +++  + K +G  + L DINL +EDGEFVVFVGPSGCGKSTLLR ++GLE  ++G I
Sbjct: 1   MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            IGG+ VTT  PA R +AMVFQSYALYPH++VRENM   +K      +    R+AEA+R+
Sbjct: 61  EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L LEDYLDR+P +LSGGQRQRVAIGRA+V+ P +FLFDEPLSNLDA LR+  R+E+  LH
Sbjct: 121 LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           +QL A+MIYVTHDQ+EAMT+ADKIVVL  GRIEQVG+PM+LY+ P +RFVAEFIG+PAMN
Sbjct: 181 KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN 240

Query: 241 F----VPAQRLG-GNPGQFIGIRPEYARISPVGP--LAGEVIHVEKLGGDTNILVDMGED 293
                V  Q +       F+G RPE+  I P G   +A  V   E+LGG++ + + +   
Sbjct: 241 VFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGG 300

Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLSFDEAGQRI 331
               AR+ G  +T VG  +   F       FDEAG+ I
Sbjct: 301 GQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI 338


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: 388
Number of extensions: 15
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: 331
Length of database: 338
Length adjustment: 28
Effective length of query: 303
Effective length of database: 310
Effective search space:    93930
Effective search space used:    93930
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