GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Synechococcus elongatus PCC 7942

Align AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate Synpcc7942_0247 Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Query= TCDB::Q52813
         (400 letters)



>FitnessBrowser__SynE:Synpcc7942_0247
          Length = 377

 Score =  228 bits (580), Expect = 3e-64
 Identities = 137/369 (37%), Positives = 207/369 (56%), Gaps = 15/369 (4%)

Query: 27  YRSIFYQILTIVILVGFVWWVAHNTAVNLARSNTASGFGFLRGRAGFEIGQSLITFSSDS 86
           +R ++  ++ +V+ +G +W V  N   NL++   +  F +L   AGF IG+S I + +  
Sbjct: 18  WRWVWQLLVLLVVGLGAIWLV-DNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTAD 76

Query: 87  TYARALLVGILNTLLVAVTGIFTATIIGFLIGIGRLSRNWLIAKLCTVYVEVFRNIPPLL 146
           +YARAL+VG++N+L V   G+   T+IG L G+   S NWL+ +L   YV V RN P LL
Sbjct: 77  SYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLL 136

Query: 147 VIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLAFPKPIFDTGMIAVGIALVIAIVASII 206
            +  WY  +L  LP  ++      S+YL+ +G+  P P         G  +VI  +A ++
Sbjct: 137 QLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQ------TPGWLVVILAIALVL 190

Query: 207 IARWAHKRQAATGQPFHTVWTAIALIVGLPLLVFVVSGFPLTFDVPVAGKFNLTGGSVVG 266
              W  +RQ +  + +  ++ AIA++  L LL  +   +P            + GG  + 
Sbjct: 191 FVSWLAQRQRSP-RDWRWLYGAIAVVTVLMLLTQL--SWPQQLQPG-----QIRGGLRLS 242

Query: 267 PEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQSEAAGALGLHPSSVTRLVVVPQALRII 326
            EF +L L L  YT +FI EI+RGGI  VP GQ EAA ALGL  S     +VVPQALR+I
Sbjct: 243 LEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVI 302

Query: 327 IPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTILNQSGQAIEIVCIWGIVYLSLSILTSL 386
           +P L SQY+   KNSSLAIA+G+ DL A   T LNQ+G+ +E+  I  + YL+++ + S 
Sbjct: 303 VPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISA 362

Query: 387 FMNWFNAKM 395
            MN    ++
Sbjct: 363 GMNGLQQRL 371


Lambda     K      H
   0.327    0.141    0.432 

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: 483
Number of extensions: 22
Number of successful extensions: 2
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: 400
Length of database: 377
Length adjustment: 30
Effective length of query: 370
Effective length of database: 347
Effective search space:   128390
Effective search space used:   128390
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: 50 (23.9 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