GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Synechococcus elongatus PCC 7942

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__SynE:Synpcc7942_0513
          Length = 250

 Score =  134 bits (336), Expect = 2e-36
 Identities = 88/245 (35%), Positives = 132/245 (53%), Gaps = 19/245 (7%)

Query: 19  KSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIFDGEPIQQL 78
           KS+G    V    + VAQG + GL+GPNGAGKTT F + +   RPD+G V  D   + +L
Sbjct: 18  KSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETELTRL 77

Query: 79  QPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVVKEEKQLQE 138
              Q A+ G+    Q A     L+V+EN+LL  Q QTG           +  +E++Q  E
Sbjct: 78  PMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQ-QTG-----------IRGREQRQRVE 125

Query: 139 QAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMT---NPKLILLDEPAAGVNPRLI 195
           +   LL    L K A+     +SGG+R+  E+ RAL      PK +LLDEP AG++P  +
Sbjct: 126 E---LLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAV 182

Query: 196 DDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTNSQVLE 255
            ++   I+   R   M  LI +HN+   + + DR ++L +G+ LA G+  E+ +N  V +
Sbjct: 183 AEV-QEIIARLRAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQ 241

Query: 256 AYLGK 260
            YLG+
Sbjct: 242 YYLGE 246


Lambda     K      H
   0.319    0.136    0.391 

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: 125
Number of extensions: 7
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: 260
Length of database: 250
Length adjustment: 24
Effective length of query: 236
Effective length of database: 226
Effective search space:    53336
Effective search space used:    53336
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 (21.7 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