GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Synechococcus elongatus PCC 7942

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__SynE:Synpcc7942_0513
          Length = 250

 Score =  117 bits (292), Expect = 3e-31
 Identities = 73/221 (33%), Positives = 116/221 (52%), Gaps = 5/221 (2%)

Query: 20  ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79
           I+  ++ S+A GE+V ++GPNGAGK+T      GL  P +G +      +T L   Q  R
Sbjct: 25  IVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETELTRLPMTQRAR 84

Query: 80  RGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP--KLAQRRNQRAGTL 137
            G+ Y+ Q  ++F  LTV ENL +         +  + R+  +    +L +  + +   +
Sbjct: 85  LGIGYLAQEASIFRHLTVVENLLLVLQQTGIRGREQRQRVEELLSEFRLEKVAHTQGIRV 144

Query: 138 SGGERQMLAMGRALMLD---PDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQ 194
           SGGER+   + RAL +    P  LLLDEP A + PI V +V   I  + A    I++ + 
Sbjct: 145 SGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAEVQEIIARLRAQQMGILITDH 204

Query: 195 NAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
           N ++ L + DR Y+L +G     GS + L ++PLV + YLG
Sbjct: 205 NVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYYLG 245


Lambda     K      H
   0.320    0.139    0.393 

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: 124
Number of extensions: 8
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: 240
Length of database: 250
Length adjustment: 24
Effective length of query: 216
Effective length of database: 226
Effective search space:    48816
Effective search space used:    48816
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