GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Synechococcus elongatus PCC 7942

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__SynE:Synpcc7942_0513
          Length = 250

 Score =  111 bits (277), Expect = 2e-29
 Identities = 81/263 (30%), Positives = 137/263 (52%), Gaps = 34/263 (12%)

Query: 15  LKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITFN 74
           +++E++   +G  + +N  S    +G++  L+GPNGAGKTT F   TG  +P  G +  +
Sbjct: 11  IRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLD 70

Query: 75  QKSGKQYLLERLPDFRITKEARVARTF--QNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132
           +       L RLP   +T+ AR+   +  Q   +F  LTV+ENLL+             +
Sbjct: 71  ETE-----LTRLP---MTQRARLGIGYLAQEASIFRHLTVVENLLL-------------V 109

Query: 133 LGLIGV-GPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT--- 188
           L   G+ G  +R+  E + L+ F LEK      A      +  G +RR EIARA+     
Sbjct: 110 LQQTGIRGREQRQRVEEL-LSEFRLEKV-----AHTQGIRVSGGERRRTEIARALAVGSQ 163

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
           GP+ L LDEP AG++P   A +  ++  +RA+    IL+ +H++   ++I+D   +L  G
Sbjct: 164 GPKFLLLDEPFAGIDPIAVAEVQEIIARLRAQQ-MGILITDHNVRETLKITDRAYILRDG 222

Query: 249 QKISDGTPDHVKNDPRVIAAYLG 271
           + ++ G+ + + ++P V   YLG
Sbjct: 223 EILAAGSAEELASNPLVRQYYLG 245


Lambda     K      H
   0.318    0.136    0.386 

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: 158
Number of extensions: 10
Number of successful extensions: 5
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: 292
Length of database: 250
Length adjustment: 25
Effective length of query: 267
Effective length of database: 225
Effective search space:    60075
Effective search space used:    60075
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: 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