GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Synechococcus elongatus PCC 7942

Align 6-phosphofructokinase isozyme 1; EC 2.7.1.11 (characterized)
to candidate Synpcc7942_0592 Synpcc7942_0592 6-phosphofructokinase

Query= CharProtDB::CH_024070
         (320 letters)



>FitnessBrowser__SynE:Synpcc7942_0592
          Length = 360

 Score =  184 bits (468), Expect = 2e-51
 Identities = 120/314 (38%), Positives = 183/314 (58%), Gaps = 26/314 (8%)

Query: 2   IKKIGVLTSGGDAPGMNAAIRGVVRSALTE-GLEVMGIYDGYLGLYEDRMVQL-----DR 55
           ++K+GVLTSGGD PG+NA IR + R A+   G E+ GI     GL + + + L     DR
Sbjct: 3   VRKLGVLTSGGDCPGLNAVIRAIARHAVGNYGWELWGIAYATQGLLKRQAIALSPHHFDR 62

Query: 56  YSVSDMINRGGTFLGSARFPEFRDENI--RAVAIENLKKRGIDALVVIGGDGSYMGAMRL 113
            S+  ++  GGT LGS      R + +  +A  +   ++ G+DAL+ IGGDGS     +L
Sbjct: 63  QSLDPLLCSGGTILGSIN----RGDTLAHQAEILAGYQELGLDALIGIGGDGSLAILRQL 118

Query: 114 TEMG-FPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGR 172
            E G +  IG+P TIDND+  T+  IGF TA+ TV EA+  L  T++SH RI + EVMGR
Sbjct: 119 AEAGRWQFIGIPKTIDNDVALTERAIGFDTAIHTVAEALLSLGSTAASHDRIMIAEVMGR 178

Query: 173 YCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAK-GKKHAIVAI---TEHMCDV 228
             G L L   IAGG + +++PE+ +   +L + ++    +  +++A++AI   T H  +V
Sbjct: 179 QSGHLALQGGIAGGADVILLPEIPYRLLELCHYLQQLRDRWQRRYAVIAIAEGTHHPPEV 238

Query: 229 --------DELAHFI-EKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAG 279
                   ++L   I  ++   + R TVLGH+QRGG+PV  DR+LA++MG  A++ L AG
Sbjct: 239 TQGPGSLGEQLVQAITAQDPTLDARVTVLGHVQRGGNPVASDRLLATQMGYAAVERLAAG 298

Query: 280 YGGRCVGIQNEQLV 293
             G  +  Q  ++V
Sbjct: 299 ASGEMMAWQGGRVV 312


Lambda     K      H
   0.322    0.141    0.413 

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: 344
Number of extensions: 18
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: 320
Length of database: 360
Length adjustment: 28
Effective length of query: 292
Effective length of database: 332
Effective search space:    96944
Effective search space used:    96944
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: 49 (23.5 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