GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_2630
          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:

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