GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Dinoroseobacter shibae DFL-12

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>FitnessBrowser__Dino:3608728
          Length = 376

 Score =  136 bits (342), Expect = 7e-37
 Identities = 82/243 (33%), Positives = 133/243 (54%), Gaps = 17/243 (6%)

Query: 11  KRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLV 70
           KR+GS   +K    +   G+ ++I+GSSG GK+T LR +  LE P  G I L+ E++   
Sbjct: 22  KRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEGAIYLDGEQVNGK 81

Query: 71  ANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKA 130
           A  D                   MV+Q   L+  +T  EN+ E  + + G+ K E R++A
Sbjct: 82  ATWD---------------RDTPMVWQSLALFPFLTVQENV-EFALKMRGIGKEERRQRA 125

Query: 131 EHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLK 190
           + +L+K+ +    D     +SGG++QRVA+ARAL  EP+++L DEP SALD  L   +  
Sbjct: 126 DKWLDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQS 185

Query: 191 VMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFL 249
           V+  L ++ G T V VTH M  A  +++++V + +G +E+ G P E+   P +  + +FL
Sbjct: 186 VLSNLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFL 245

Query: 250 SGS 252
             +
Sbjct: 246 GSA 248


Lambda     K      H
   0.317    0.131    0.366 

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: 175
Number of extensions: 7
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: 254
Length of database: 376
Length adjustment: 27
Effective length of query: 227
Effective length of database: 349
Effective search space:    79223
Effective search space used:    79223
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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