GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2560 in Synechococcus elongatus PCC 7942

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Synpcc7942_1490 Synpcc7942_1490 nitrate transport ATP-binding subunits C and D

Query= reanno::acidovorax_3H11:Ac3H11_2560
         (259 letters)



>FitnessBrowser__SynE:Synpcc7942_1490
          Length = 663

 Score =  196 bits (497), Expect = 1e-54
 Identities = 102/246 (41%), Positives = 155/246 (63%), Gaps = 4/246 (1%)

Query: 4   VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63
           V+++ + + F  + G    AL+ +D E++  +F++++G SGCGKSTLL ++AGL+  T G
Sbjct: 5   VAVENIEKSFPLSGGNEYLALKGIDLEIKQGEFISLIGHSGCGKSTLLNLIAGLELPTDG 64

Query: 64  RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRE--RGMPEAQQKERAAYFIA 121
            V L+G  +  PG +R +VFQ+Y+LFPWLT+ +NI   + E  R +P+ +++      I 
Sbjct: 65  AVSLEGQQITAPGPDRMVVFQNYSLFPWLTVRENIALAVDEVLRDLPKEERQAIVEEHIQ 124

Query: 122 KVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGI 181
            VGL       P QLSGGM+QR AIAR LA  PK+LL+DEPFGALD  TR  +QE L+ I
Sbjct: 125 LVGLGHAADKPPAQLSGGMKQRVAIARGLATRPKLLLLDEPFGALDALTRGNLQEKLMQI 184

Query: 182 WEAERKTVLFVTHDIDEAIFMANRVAVFSARPG-RIKTELAVDLPHPR-HYTIKTSPEFM 239
            E    T + VTHD+DEA+ +++R+ + +  PG +I   L VD+P PR    +   P + 
Sbjct: 185 CEENHVTAVMVTHDVDEAVLLSDRIVMLTNGPGSKIGGILEVDIPRPRKRMDVVHHPSYY 244

Query: 240 DLKARL 245
            L++ +
Sbjct: 245 SLRSEI 250


Lambda     K      H
   0.322    0.136    0.394 

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: 390
Number of extensions: 20
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: 259
Length of database: 663
Length adjustment: 31
Effective length of query: 228
Effective length of database: 632
Effective search space:   144096
Effective search space used:   144096
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 (21.9 bits)
S2: 50 (23.9 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