GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Synechococcus elongatus PCC 7942

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Synpcc7942_1347 Synpcc7942_1347 2-hydroxyacid dehydrogenase-like

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__SynE:Synpcc7942_1347
          Length = 331

 Score =  153 bits (386), Expect = 7e-42
 Identities = 97/288 (33%), Positives = 146/288 (50%), Gaps = 24/288 (8%)

Query: 48  ALVTLVTDKVDKELLENAPKLKI--IAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATA 105
           A+ + V D++D   LE   +L +  +A    G++ +D+  A + G+ V   P     A A
Sbjct: 47  AVCSFVNDRLDAITLEALAELGVEHVALRCAGFNQVDLSAAERLGLRVVRVPAYSPHAVA 106

Query: 106 DLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQAL 165
           + A AL+L + R+I  A A  R G +    +       +G+ L G T+GI+G GRIG  L
Sbjct: 107 EHAIALILTLNRKIHRAYARTREGNFALDGL-------VGFDLNGCTVGIIGTGRIGAVL 159

Query: 166 AKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEK 225
            +  +GFG  ++ +     P+     GA Y D + L +E+  ISLH PLT +TYH++  +
Sbjct: 160 TQILRGFGCHVLAHDLVENPDCLAA-GAVYTDLDQLWQEAQIISLHCPLTPQTYHLVNRE 218

Query: 226 ELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFE-EEPYYNEE-------- 276
            +  M+P  +LINTSRG +VDT A+I+ LK   I   GLDV+E EEP + ++        
Sbjct: 219 AIAKMQPGTMLINTSRGGLVDTQAVIEGLKLKRIGALGLDVYEQEEPLFFQDHSTEIIHD 278

Query: 277 -----LFKLKNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPN 319
                L    NVV+  H    T  A   +AE    NL    +G   PN
Sbjct: 279 DVFQRLLTFPNVVITGHQAFLTDTALHNIAETTLSNLTDLEQGRACPN 326


Lambda     K      H
   0.317    0.137    0.392 

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: 219
Number of extensions: 12
Number of successful extensions: 4
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: 331
Length of database: 331
Length adjustment: 28
Effective length of query: 303
Effective length of database: 303
Effective search space:    91809
Effective search space used:    91809
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 (21.6 bits)
S2: 49 (23.5 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