GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Synechococcus elongatus PCC 7942

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  152 bits (383), Expect = 1e-41
 Identities = 83/250 (33%), Positives = 149/250 (59%), Gaps = 23/250 (9%)

Query: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVS 67
           +++  + K++G  + +K + LT   G ++++LG SGSGKST LR I  LE P  G+I ++
Sbjct: 3   IQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLT 62

Query: 68  GEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNV---IEAPRRVLG 124
           G +   +  ++                ++GFVFQ++ L+ H+++  N+   +E  +    
Sbjct: 63  GRDATNESVRD---------------RQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKE 107

Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184
           K +A   E+ E L+   G+ D+   YP+QLSGGQ+QR A+AR LA+QP+V+L DEP  AL
Sbjct: 108 KVRARVEELLE-LVQLTGLGDR---YPSQLSGGQRQRVALARALAVQPQVLLLDEPFGAL 163

Query: 185 DPEMVQEVLNVIRALAEEGR-TMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFEN 243
           D ++ +++ + +R L +E   T + VTH+   A +V+ ++V ++ G VE+ G+P ++++N
Sbjct: 164 DAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDN 223

Query: 244 PQSARCKQFM 253
           P +     F+
Sbjct: 224 PATPFVMSFI 233


Lambda     K      H
   0.317    0.133    0.367 

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: 194
Number of extensions: 9
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: 257
Length of database: 338
Length adjustment: 26
Effective length of query: 231
Effective length of database: 312
Effective search space:    72072
Effective search space used:    72072
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: 48 (23.1 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