GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Synechococcus elongatus PCC 7942

Align NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_1894 Synpcc7942_1894 integral membrane protein of the ABC-type Nat permease for neutral amino acids

Query= TCDB::P74455
         (372 letters)



>FitnessBrowser__SynE:Synpcc7942_1894
          Length = 359

 Score =  340 bits (873), Expect = 3e-98
 Identities = 179/370 (48%), Positives = 247/370 (66%), Gaps = 14/370 (3%)

Query: 4   GYLIFLITSAATYGIFALGLNLQWGFAGLINFGHVAFMTLGAYATTLLSLRGLPIPLAVL 63
           GY+I L+ + A + +F +GLNL WG+ GL+NFGHVAF+ +GAY+ +LL+ +G P+ LA +
Sbjct: 3   GYIILLVCTIALFALFCVGLNLHWGYTGLLNFGHVAFLLIGAYSVSLLAQQGWPLWLAAI 62

Query: 64  VGMGLAMALGLLIGTSTLRLREDYLAIVTIGVSELIRLIANNEEWLTQGTFGVQSFPWPM 123
            G+ LA  LGL++G ++LRL +DYL IVT+G++E++R+   NE  LTQG+FGVQ++P  +
Sbjct: 63  AGVTLAALLGLVMGVASLRLSQDYLGIVTVGLAEVLRIFVQNETGLTQGSFGVQAYPIIL 122

Query: 124 D-FNPTLLSRIVFVIWLTVLTIYAESILIKSLLKQWKEGKKIQGKSYQPRKPLALLIWGI 182
             + P +    + V+ L  +  +         L QW      +GK +     LA++  G 
Sbjct: 123 QGWEPPIWQTHLLVVGLLAIAAWGYW-----QLWQWWRSSASRGKHW-----LAIVALG- 171

Query: 183 ITTALILTAYVPGVVSLYNYSGKAGLMLLALTLLALTYAGLEFWVHSPWGRILKAIREDE 242
            ++ ++L     G+     Y  ++G MLL L  L LT A ++  V SPWGR+LKAIREDE
Sbjct: 172 -SSLIVLPPAALGLADYERYP-RSGQMLLLLGALWLTVAAVDRLVRSPWGRVLKAIREDE 229

Query: 243 EIPRALGKNVFWYKLQAFMGGGAIAGLAGALFAWQLTSIYPSNFDTLLTFNAWIIVVLGG 302
            +  ALGKNV  YKLQ+   GGAIAGLAG  +AWQLT+IYP NF   LTF+ W ++VLGG
Sbjct: 230 TVAIALGKNVLSYKLQSLALGGAIAGLAGVFYAWQLTAIYPDNFRPQLTFDVWTMLVLGG 289

Query: 303 AGSNAGTVLGTIIFWAYDSLTRFLLPQIAFLDQSQAGALRVMVIGLILMVLMVWRPQGIL 362
                G VLG  +FW YDSLTRFLLP I  LD SQ GALR+ ++GL+LM LM+WRPQGIL
Sbjct: 290 TAHRFGPVLGAAVFWLYDSLTRFLLPAILPLDGSQIGALRIALVGLLLMALMIWRPQGIL 349

Query: 363 GKKEELTLGR 372
           G++EEL+LGR
Sbjct: 350 GRREELSLGR 359


Lambda     K      H
   0.327    0.143    0.442 

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: 462
Number of extensions: 15
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: 1
Length of query: 372
Length of database: 359
Length adjustment: 30
Effective length of query: 342
Effective length of database: 329
Effective search space:   112518
Effective search space used:   112518
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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