GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Erythrobacter gangjinensis K7-2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_047006707.1 AAW01_RS07015 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>NCBI__GCF_001010925.1:WP_047006707.1
          Length = 317

 Score =  110 bits (276), Expect = 3e-29
 Identities = 78/256 (30%), Positives = 124/256 (48%), Gaps = 33/256 (12%)

Query: 7   EVVLKVAGISKRFGGLQ------ALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYT 60
           +  +++  + K + G        AL  V   + +G V+GL+GPNGAGK+T  N++ GL  
Sbjct: 3   DAAIEIRDLRKEYAGSAKAPPKLALKGVSFDVPQGSVFGLLGPNGAGKSTLINIMAGLVN 62

Query: 61  PDAGTFELAGKPYEPTAVHEVAKAGIARTFQNI---RLFAEMTALENVMVGRHIRTGSGL 117
              GT  + G+  +    H  AK  I    Q I     F     LEN          SG 
Sbjct: 63  KTGGTVRIWGRDIDED--HRNAKLNIGIVPQEIVFDPFFTPYEVLENQ---------SGF 111

Query: 118 FGAVFRTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQ 177
           +G            A   +R++ELL  V +    D  ARTLS G +RRL IA+A+   P 
Sbjct: 112 YGI-----------AKALRRSEELLRAVRLEDKRDAYARTLSGGMKRRLLIAKAMVHSPP 160

Query: 178 LIALDEPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIA 237
           ++ LDEP AG++   + QL EL+  +  +  T++L  H ++    LC+++ ++++G+ IA
Sbjct: 161 ILVLDEPTAGVDVELRKQLWELVGELNAEGVTVVLTTHYLEEAEELCEQIAIINHGELIA 220

Query: 238 EGNPAEV--QKNEKVI 251
                E+     EK+I
Sbjct: 221 NKPTRELVGMMGEKII 236


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: 199
Number of extensions: 9
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: 260
Length of database: 317
Length adjustment: 26
Effective length of query: 234
Effective length of database: 291
Effective search space:    68094
Effective search space used:    68094
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 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