GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP in Escherichia coli BW25113

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 14258 b0112 aromatic amino acid transporter (NCBI)

Query= TCDB::F2HQ25
         (459 letters)



>FitnessBrowser__Keio:14258
          Length = 457

 Score =  296 bits (757), Expect = 1e-84
 Identities = 158/463 (34%), Positives = 261/463 (56%), Gaps = 21/463 (4%)

Query: 1   MENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFF 60
           ME  Q   + +RGL+NRHIQLIA+ G IGTGLFLG+   IQ  GP +I  Y + G   F 
Sbjct: 2   MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61

Query: 61  FLRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFW 120
            +R +GEM+  +P   SF +F  KY G   G+ + W+YW++ V V ++ELTA+G YIQFW
Sbjct: 62  IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121

Query: 121 LPQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIV-TAIILVAGNFH 179
            P++P W+   V   ++  +N  N + FGE EFWFA+IKV A++ MI+    +L +GN  
Sbjct: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGN-- 179

Query: 180 YSTVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNP 239
                        A++SN++D     PHG    V  + ++MF+F  +E +G+TAAE  NP
Sbjct: 180 ---------GGPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNP 230

Query: 240 KKSLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINF 299
           ++S+PKA NQ+  RIL+FY+G+L  ++++  W  + AD SPFV++F  +G  + A  +N 
Sbjct: 231 EQSIPKATNQVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNI 290

Query: 300 VVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAP 359
           VVLT+A S  NS ++  +R ++ LAQQ +  +      + K G+P+N + ++  ++ L  
Sbjct: 291 VVLTAALSVYNSCVYCNSRMLFGLAQQGNAPK--ALASVDKRGVPVNTILVSALVTALCV 348

Query: 360 VLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPKPQITVP-- 417
           ++  +   ++AF    +   +  ++ + +    + ++R+++    +G +T  P +  P  
Sbjct: 349 LINYLAP-ESAFGLLMALVVSALVINWAMISLAHMKFRRAK--QEQGVVTRFPALLYPLG 405

Query: 418 -FIVAIF-AIVFASLFFNADTFYPALGAIVWTIFFGLYSHYKK 458
            +I  +F A V   +              VW I  G+   +K+
Sbjct: 406 NWICLLFMAAVLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKE 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: 597
Number of extensions: 25
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: 459
Length of database: 457
Length adjustment: 33
Effective length of query: 426
Effective length of database: 424
Effective search space:   180624
Effective search space used:   180624
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