GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0327 in Synechococcus elongatus PCC 7942

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like

Query= TCDB::Q72KX3
         (369 letters)



>FitnessBrowser__SynE:Synpcc7942_0526
          Length = 293

 Score = 97.1 bits (240), Expect = 5e-25
 Identities = 93/353 (26%), Positives = 156/353 (44%), Gaps = 82/353 (23%)

Query: 1   MRDRILAFLVLLPSVLAVGVFVYGFIGQNLWVSLTDWGKDPAQALALRPELRFVGLENYR 60
           +RDR+  +L L P++  +G+ V+    Q  + S T +  +      L    ++VGLEN++
Sbjct: 4   LRDRLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYN------LTRSPQWVGLENFQ 57

Query: 61  ELFTGFVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMAL 120
            L     D  F +++ N    T  ++ G + L                    VFL P+ L
Sbjct: 58  RLLN---DAVFWKTLGN----TFIYLIGVVPL-------------------LVFL-PLGL 90

Query: 121 SFVVTGTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGL 180
           + +V         +P  G+    TLF                      RL +YT ++V +
Sbjct: 91  AILVN--------RPLRGI----TLF----------------------RLAYYTPVIVSI 116

Query: 181 VLLYVAYTAYREGERRRALWGLASAGVL-LLWAFAFGQGLRLLPYPEVHGFSLALVGVIL 239
           V+  +A+            W  A  G+L  L    FG+G +  P P +   +LAL  V+ 
Sbjct: 117 VVAGIAWR-----------WLYAETGLLNQLGQLVFGEGFQ--PIPWLTSPALALFSVMA 163

Query: 240 AAVWQMSGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLG 299
             VW+  GY M +YLAGL+GIP+E+ EAA +DG+  W+    +  P++ P  +   ++  
Sbjct: 164 VTVWKGLGYYMVIYLAGLQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISA 223

Query: 300 HIALKIFDLVFAMA-GLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLV 351
             A K+F+ VF M  G     +     Y+Y  AF+  + +    +G+ L L+V
Sbjct: 224 ISATKVFEEVFIMTQGGPLNSSKTVVYYVYQQAFQKLEVSYACTVGLALFLVV 276


Lambda     K      H
   0.331    0.146    0.458 

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: 291
Number of extensions: 19
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 293
Length adjustment: 28
Effective length of query: 341
Effective length of database: 265
Effective search space:    90365
Effective search space used:    90365
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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