GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SynE:Synpcc7942_1894 Synpcc7942_1894 integral
           membrane protein of the ABC-type Nat permease for
           neutral amino acids
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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