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_0249 Synpcc7942_0249 ATPase

Query= TCDB::Q9HU32
         (257 letters)



>FitnessBrowser__SynE:Synpcc7942_0249
          Length = 261

 Score =  226 bits (576), Expect = 4e-64
 Identities = 120/243 (49%), Positives = 165/243 (67%), Gaps = 12/243 (4%)

Query: 13  LHKRYGD-LEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQILVSGEEL 71
           + K YG+  + L G+SLT + G+V+ ++G SGSGKSTFLR +N LE+  +G+I + G  L
Sbjct: 27  VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86

Query: 72  RLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLGKSKAEAI 131
                      + D + I  +R E+G VFQ FNL+PH+++L N++ AP +V     A+A 
Sbjct: 87  -----------SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135

Query: 132 EIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEMVQE 191
             A  LL +V IA++   YP QLSGGQQQR AIAR LAMQP+++LFDEPTSALDPEMV+E
Sbjct: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195

Query: 192 VLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENPQSARCKQ 251
           VL+V+R LA EG TML+ THE+ FAR+V+  VV +  G + E+  P + F  PQS R KQ
Sbjct: 196 VLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQ 255

Query: 252 FMS 254
           F++
Sbjct: 256 FLA 258


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: 176
Number of extensions: 4
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: 257
Length of database: 261
Length adjustment: 24
Effective length of query: 233
Effective length of database: 237
Effective search space:    55221
Effective search space used:    55221
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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