GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Dinoroseobacter shibae DFL-12

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3608587 Dshi_1981 ABC transporter related (RefSeq)

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Dino:3608587
          Length = 257

 Score =  185 bits (469), Expect = 9e-52
 Identities = 102/254 (40%), Positives = 144/254 (56%)

Query: 7   EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66
           E +L   G++  FG  +AL  V + +  G + GLIGPNGAGK+T FNV+TG   P +GT 
Sbjct: 3   EPILATHGLTHDFGPFRALHGVSLEVAPGTMTGLIGPNGAGKSTLFNVLTGALRPTSGTV 62

Query: 67  ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126
            L G          + +AG+AR+FQ  R FA MT LENVM+    + G  ++GA    + 
Sbjct: 63  TLQGTDITGQPPDALFRAGLARSFQIPRPFARMTVLENVMLAPKAQIGERVWGAFLNPRA 122

Query: 127 FKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAA 186
             A+E AI ++A E+L++V + K AD  A  +S G  + LE+AR L  DP LI LDEPAA
Sbjct: 123 MAAQENAIRQKAMEVLEFVTLAKLADQAAGEISGGQMKLLELARVLMGDPTLILLDEPAA 182

Query: 187 GMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQK 246
           G+N      L + I+ +     T ++IEHD+  VM  C  V  L  G+ I EG P +   
Sbjct: 183 GVNPALTEVLIDKIETLNRTGTTFVIIEHDMDFVMQHCTPVIALGQGRVIFEGTPEQALA 242

Query: 247 NEKVIEAYLGTGGH 260
           +  +++AYLG   H
Sbjct: 243 DPVLLDAYLGAQAH 256


Lambda     K      H
   0.319    0.137    0.384 

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: 201
Number of extensions: 10
Number of successful extensions: 1
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: 260
Length of database: 257
Length adjustment: 24
Effective length of query: 236
Effective length of database: 233
Effective search space:    54988
Effective search space used:    54988
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 (21.7 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