GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natC in Synechococcus elongatus PCC 7942

Align NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Synpcc7942_1894 Synpcc7942_1894 integral membrane protein of the ABC-type Nat permease for neutral amino acids

Query= TCDB::Q8YY08
         (377 letters)



>FitnessBrowser__SynE:Synpcc7942_1894
          Length = 359

 Score =  353 bits (907), Expect = e-102
 Identities = 190/383 (49%), Positives = 262/383 (68%), Gaps = 30/383 (7%)

Query: 1   MIEYLIFLAISTATFALFSLGLNLQWGFTGLINFGHIAFMTLGAYTTVLLSLKGVPLFIS 60
           MI Y+I L  + A FALF +GLNL WG+TGL+NFGH+AF+ +GAY+  LL+ +G PL+++
Sbjct: 1   MIGYIILLVCTIALFALFCVGLNLHWGYTGLLNFGHVAFLLIGAYSVSLLAQQGWPLWLA 60

Query: 61  AIVGAIFAALLGLVIGFATLRLREDYLAIVTIGTGELIRLVVNNQDLPVGDTWVSGAFGV 120
           AI G   AALLGLV+G A+LRL +DYL IVT+G  E++R+ V N+    G T   G+FGV
Sbjct: 61  AIAGVTLAALLGLVMGVASLRLSQDYLGIVTVGLAEVLRIFVQNE---TGLT--QGSFGV 115

Query: 121 QSYPIPLST-EPNLF-FRLLMIGILTLLFAVTVFSLWRWIRNAQKLQLTDATDKTSSKQE 178
           Q+YPI L   EP ++   LL++G+L +  A   + LW+W R++                 
Sbjct: 116 QAYPIILQGWEPPIWQTHLLVVGLLAIA-AWGYWQLWQWWRSS----------------- 157

Query: 179 IASRFGVGIILGLLATAIYISGVITL----YNYIPKAGLMLVSLLVLAFVFWRLEYLVRS 234
            ASR    + +  L +++ +     L    Y   P++G ML+ L  L      ++ LVRS
Sbjct: 158 -ASRGKHWLAIVALGSSLIVLPPAALGLADYERYPRSGQMLLLLGALWLTVAAVDRLVRS 216

Query: 235 PWGRVLKAIREDEEIPKAMGKNVFWYKLQSLMLGGAIAGIAGAFFAWQISAIYPDNFQPQ 294
           PWGRVLKAIREDE +  A+GKNV  YKLQSL LGGAIAG+AG F+AWQ++AIYPDNF+PQ
Sbjct: 217 PWGRVLKAIREDETVAIALGKNVLSYKLQSLALGGAIAGLAGVFYAWQLTAIYPDNFRPQ 276

Query: 295 LTFDSWIMVILGGAGNNIGSILGAVIYFAYDAITREVLPKIIPLDEARLGAFRIMCIGLI 354
           LTFD W M++LGG  +  G +LGA +++ YD++TR +LP I+PLD +++GA RI  +GL+
Sbjct: 277 LTFDVWTMLVLGGTAHRFGPVLGAAVFWLYDSLTRFLLPAILPLDGSQIGALRIALVGLL 336

Query: 355 LMVLMIWRPQGILGKKEELTLGK 377
           LM LMIWRPQGILG++EEL+LG+
Sbjct: 337 LMALMIWRPQGILGRREELSLGR 359


Lambda     K      H
   0.328    0.145    0.441 

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: 532
Number of extensions: 20
Number of successful extensions: 4
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: 359
Length adjustment: 30
Effective length of query: 347
Effective length of database: 329
Effective search space:   114163
Effective search space used:   114163
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