GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Synechococcus elongatus PCC 7942

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_2492 Synpcc7942_2492 ATPase

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__SynE:Synpcc7942_2492
          Length = 237

 Score =  199 bits (507), Expect = 3e-56
 Identities = 111/235 (47%), Positives = 153/235 (65%), Gaps = 2/235 (0%)

Query: 9   QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68
           +PLLQ++ +   YG + AL  + + +  GEIV+LIGANGAGKST +  I      + G +
Sbjct: 3   EPLLQLSQIAVNYGAVVALTDLTLEIFPGEIVALIGANGAGKSTTLRAISRLVPLQQGRI 62

Query: 69  VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK-HFAEDVEKIF 127
            ++ +D+  +P  ++    +A  PEGRR+  R +V  NL++GA     +     D+E  F
Sbjct: 63  YYDQQDLGLIPAPQLVGRGLAHCPEGRRVLARQSVRINLELGAYCRRDRIGIQTDLELQF 122

Query: 128 TLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187
             FPRL+ER  Q  GTLSGGEQQML+I RALM+RP+LLLLDEPSLGLAP IV+ IF  IR
Sbjct: 123 DRFPRLRERQNQPAGTLSGGEQQMLAIARALMSRPRLLLLDEPSLGLAPQIVQEIFSVIR 182

Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
            L E +G+T+ LVEQNA  AL+ + R YV+  G++  SG   +LL +P V+ AYL
Sbjct: 183 SLRE-QGMTILLVEQNATLALQTADRGYVLEAGQLLFSGPAADLLIDPRVKQAYL 236


Lambda     K      H
   0.320    0.137    0.387 

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: 8
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: 247
Length of database: 237
Length adjustment: 23
Effective length of query: 224
Effective length of database: 214
Effective search space:    47936
Effective search space used:    47936
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: 46 (22.3 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