GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Synechococcus elongatus PCC 7942

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__SynE:Synpcc7942_0960
          Length = 417

 Score =  288 bits (738), Expect = 1e-82
 Identities = 179/403 (44%), Positives = 230/403 (57%), Gaps = 53/403 (13%)

Query: 1   MASVTLRNIRKAYDENE---------VMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAG 51
           +A V    I K + E           V+  INL+IADGEF+V VGPSGCGKSTL+R++AG
Sbjct: 23  VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82

Query: 52  LEDISGGDLTIDGMRVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTK----- 106
           LE  S G + +   RV+ +    R IAMVFQSYALYPH+++YDN+AFGL+  G +     
Sbjct: 83  LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142

Query: 107 ---------------KPEIDAA----VRNAAKILHIDHLLDRKPKQLSGGQRQRVAIGRA 147
                          +PE +A     VR  A +L +D LLDR+PKQLSGGQ+QRVA+GRA
Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202

Query: 148 ITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKTTMIYVTHDQVEAMTLADKIVVL 207
           I R P+VFL DEPLSNLDA LR + R +   L  +L  T +YVTHDQ EAMT+ D+I VL
Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262

Query: 208 SAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGVVQSVTHDGVTVRYE---TGETQ 264
           + G+L+QV SP  +Y  PANRFVA FIGSP MN +           VTVR     T E  
Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIP----------VTVRAPLQLTTENF 312

Query: 265 RVAVEPA-----AVKQGDKVTVGIRPEHLHVG-MAEDGISARTMAVESLGDAAYLYAESS 318
           R  +  A      +  G  V +GIRPEHL VG  A   +      VE+LG   ++  E  
Sbjct: 313 RCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGAAASKNLLITVTGVEALGSDTFIAGELK 372

Query: 319 VAPDGLIARIPPLERHTKGETQKLGATPEHCHLFD-SAGKAFQ 360
            +   + AR+ P +    G+   L   P+  HLFD   GKA +
Sbjct: 373 ESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAIR 415


Lambda     K      H
   0.320    0.135    0.384 

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: 425
Number of extensions: 17
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: 369
Length of database: 417
Length adjustment: 31
Effective length of query: 338
Effective length of database: 386
Effective search space:   130468
Effective search space used:   130468
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: 50 (23.9 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