GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ans in Synechococcus elongatus PCC 7942

Align asparaginase (EC 3.5.1.1) (characterized)
to candidate Synpcc7942_0166 Synpcc7942_0166 hypothetical protein

Query= BRENDA::Q9RFN5
         (371 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0166 Synpcc7942_0166
           hypothetical protein
          Length = 317

 Score =  164 bits (414), Expect = 4e-45
 Identities = 106/315 (33%), Positives = 159/315 (50%), Gaps = 36/315 (11%)

Query: 16  RGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAKPAQALAILETEGVAGYGFDD 75
           R GI+E+SH V A V D +GR L+  GNP   +  RSA KP QAL +L+T  +  +G  D
Sbjct: 18  REGILESSHLVEAVVCDRRGRTLFIAGNPEHSSFIRSALKPLQALVVLKTGTMERFGLSD 77

Query: 76  ADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAV 135
            D+A++C+SH        +   +L K   ++  L+C      + +  RS ++        
Sbjct: 78  RDLAIICSSHKGSVEQARQAFNILWKADIDQTALQCP-----TPVGRRSPLEY------- 125

Query: 136 CSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNL 195
             NCSGKH GMLA ++      +GY    HP+Q  +   V +L  + A +     D C +
Sbjct: 126 --NCSGKHAGMLAASKQQNWPLEGYMRRSHPVQQAILSIVGDLLGIPAAEFIVARDDCGV 183

Query: 196 PTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTM 255
           PT +  L ++  +YA L+S     D+ E        L  I RAM  HP+++AGEG + T 
Sbjct: 184 PTVSMELQQMATLYAHLSS----GDSPE--------LERIQRAMTYHPDLIAGEGEFDTE 231

Query: 256 LMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELL 315
           LMR  +G LV K GA+    IG        Q+G    LG+++K++DG      AV  + L
Sbjct: 232 LMRLTEGRLVSKTGAEGVQCIG--------QVGE--GLGLAIKVQDGAKRAKIAVAIQAL 281

Query: 316 ERLGIGSPDVRSQLA 330
            ++G  SP +   LA
Sbjct: 282 RQIGWISPAIADLLA 296


Lambda     K      H
   0.319    0.134    0.397 

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: 297
Number of extensions: 10
Number of successful extensions: 5
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: 371
Length of database: 317
Length adjustment: 29
Effective length of query: 342
Effective length of database: 288
Effective search space:    98496
Effective search space used:    98496
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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