GapMind for catabolism of small carbon sources

 

Aligments for a candidate for serP1 in Dyella japonica UNC79MFTsu3.2

Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= TCDB::F2HQ25
         (459 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_2630 N515DRAFT_2630 amino
           acid/polyamine/organocation transporter, APC superfamily
          Length = 454

 Score =  292 bits (748), Expect = 1e-83
 Identities = 158/395 (40%), Positives = 229/395 (57%), Gaps = 11/395 (2%)

Query: 4   LQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLR 63
           +Q     QRGLQ RHI+L+A+   IG GLFLG+   I++ GP+++ +Y+L G+A+F  +R
Sbjct: 1   MQTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMR 60

Query: 64  TIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQ 123
            +GEM   +P   SF  +   Y G   GY T W+YW + +  CI+E+TA+G Y+  W P 
Sbjct: 61  ALGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPD 120

Query: 124 VPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTV 183
           VP W+  +  L  +  +N    + +GE EFWFAMIKV  I+ MIV    ++        V
Sbjct: 121 VPQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGV 180

Query: 184 LSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSL 243
            +G        +SN++      P+GA   + ALQMVMFA+  +E IG+TA E  NPKKS+
Sbjct: 181 PTG--------ISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSI 232

Query: 244 PKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLT 303
           P AIN +  RIL+FYVGAL  IM+I+ W+ +    SPFVM F+ +GIK AA +INFVVLT
Sbjct: 233 PDAINSVFWRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLT 292

Query: 304 SAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLTL 363
           +A S+ N  ++S  R +++LAQQ    R   F   S +GIP  A+ ++    L   +L  
Sbjct: 293 AALSSCNGGIYSTGRMLFNLAQQGQAPR--TFAVTSPSGIPNRAVLVSLVALLFGVLLNY 350

Query: 364 IPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRK 398
           +   K  F +  S  T   +  + I L T  +YR+
Sbjct: 351 LVPAK-VFVWVTSAATFGAIWTWGIVLITQMKYRR 384



 Score = 24.3 bits (51), Expect = 0.009
 Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 18/147 (12%)

Query: 3   NLQEKHEAQR--------GLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILI 54
           NL ++ +A R        G+ NR + +  +A        L  G  +    P+ +F ++  
Sbjct: 311 NLAQQGQAPRTFAVTSPSGIPNRAVLVSLVA--------LLFGVLLNYLVPAKVFVWVT- 361

Query: 55  GIAMFFFLRTIGEMLYNDPSQHSFLNFVTKYSGV-RTGYFTQWSYWLVIVFVCISELTAI 113
             A F  + T G +L         L+   +   V R  +F   SY  +   V +  L   
Sbjct: 362 SAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGY 421

Query: 114 GTYIQFWLPQVPLWLIEIVMLALLFGL 140
               +  L   PLWL+ + +L  +FGL
Sbjct: 422 FPDTRVALIVGPLWLVLLTVLYYVFGL 448


Lambda     K      H
   0.329    0.141    0.434 

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: 632
Number of extensions: 31
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: 459
Length of database: 454
Length adjustment: 33
Effective length of query: 426
Effective length of database: 421
Effective search space:   179346
Effective search space used:   179346
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 (21.8 bits)
S2: 51 (24.3 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