GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Synechococcus elongatus PCC 7942

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= TCDB::P31134
         (377 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  221 bits (564), Expect = 2e-62
 Identities = 136/332 (40%), Positives = 196/332 (59%), Gaps = 31/332 (9%)

Query: 19  LLEIRNLTKSYDGQH--AVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQI 76
           +L +  + K + G    AVD VS  +  GEI  L+G SGCGK+TLLRM+AGFE   +G I
Sbjct: 6   VLCLDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSI 65

Query: 77  MLDGVDLS----QVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNE 132
            L G  ++     +PP  R + M+FQ YALFPH+TV  N+ FGL+ D+   A +A    +
Sbjct: 66  QLAGETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLR-DRKGSAAVA---RQ 121

Query: 133 MLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEV 192
            L LV ++   +R PH+LSGGQ+QRVALAR+LA +P L+LLDEP+  LD ++R R++ E+
Sbjct: 122 ALALVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQEL 181

Query: 193 VDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGS 252
            DIL +   T ++VTHDQEEA+++  R+A+M  G+F QIG+PEE+++HP +R+ AEF+  
Sbjct: 182 RDILRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ 241

Query: 253 VNVFEGVLKERQEDG--LVL---DSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEE 307
            N    +  E Q D    VL   ++PG         + S     P  V +R E ++L   
Sbjct: 242 ANF---LATEYQGDAWRTVLGDFEAPG-------GLEGSRTGGEPPVVMVRQEDVLLHPH 291

Query: 308 PPANGCNFAVGEVIHIAYLGDLSVYHVRLKSG 339
           P   G       V    +LG    Y V+L +G
Sbjct: 292 PEGTGL------VRDRQFLGRDYRYFVQLPAG 317


Lambda     K      H
   0.321    0.137    0.400 

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: 366
Number of extensions: 19
Number of successful extensions: 3
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: 377
Length of database: 368
Length adjustment: 30
Effective length of query: 347
Effective length of database: 338
Effective search space:   117286
Effective search space used:   117286
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