GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Synechococcus elongatus PCC 7942

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Synpcc7942_2574 Synpcc7942_2574 ATPase

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__SynE:Synpcc7942_2574
          Length = 251

 Score = 87.4 bits (215), Expect = 3e-22
 Identities = 80/271 (29%), Positives = 120/271 (44%), Gaps = 37/271 (13%)

Query: 1   MTTQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGF 60
           M+  S    P L   HL+  +     + DV+     G++  I+GPNGAGK+T    + G 
Sbjct: 1   MSQASAPNPPTLQAHHLSASYRDREVLQDVNLQLRAGQVVGIVGPNGAGKSTFLKALLGL 60

Query: 61  YTPTVGRLTLRHADGKEFLLERMPGYR-ISQKASV----ARTFQNIRLFGGMSVLENLIV 115
             P  G +  R       L  R+P    + Q+A V      T  ++ L G         V
Sbjct: 61  -VPHQGEVFWRGLP----LASRLPHVAYVPQRAQVDFDYPATVWDVVLMGR--------V 107

Query: 116 AQHNKLIRASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQR 175
           AQ   L R S  S              ++AV  A   LDRV L +      G L  G Q+
Sbjct: 108 AQTGWLRRFSAAS--------------QQAVKAA---LDRVELWDLRSRPIGELSGGQQQ 150

Query: 176 RLEIARAMCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTI 235
           R+ IAR++  E  +  LDEP AG++ R  G L ++L  +  +   GV+++ HD+   +  
Sbjct: 151 RVFIARSLAQEAELFLLDEPFAGIDRRSEGLLYEILRDLAQQGH-GVVVVHHDLGQAIQQ 209

Query: 236 SDHVVVLDYGRKISDGDPAFVKNDPAVIRAY 266
            D +V+L+  R I+ G P  V     + RAY
Sbjct: 210 FDELVLLNQ-RVIAQGHPRLVLQPDHLARAY 239


Lambda     K      H
   0.319    0.137    0.397 

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: 149
Number of extensions: 9
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: 294
Length of database: 251
Length adjustment: 25
Effective length of query: 269
Effective length of database: 226
Effective search space:    60794
Effective search space used:    60794
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: 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