GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP in Escherichia coli BW25113

Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate 14712 b0576 phenylalanine transporter (NCBI)

Query= TCDB::F2HQ24
         (457 letters)



>FitnessBrowser__Keio:14712
          Length = 458

 Score =  290 bits (743), Expect = 5e-83
 Identities = 158/463 (34%), Positives = 272/463 (58%), Gaps = 26/463 (5%)

Query: 2   NTNQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMY 61
           +T  N+E     RGL NRHIQLIA+ G IGTGLFLG G +I + GP+++  Y + G + +
Sbjct: 10  DTASNQE-PTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAF 68

Query: 62  ILLRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINF 121
           +++R +GEM+ ++P   SF +F  +Y G   G+   W+Y ++ V V MAEL A G Y+ +
Sbjct: 69  LIMRQLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQY 128

Query: 122 WLPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYH 181
           W PD+P W+      +++  +N +N + +GETEFWF +IK++AIIG+I   + L+FS + 
Sbjct: 129 WFPDVPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLFSGH- 187

Query: 182 TGTDTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAI 241
            G +  S+ N+ +   FF  G +    S  ++MF+F  +E IG+TAAE  +P  ++ KA+
Sbjct: 188 -GGEKASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAV 246

Query: 242 NQIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAAS 301
           NQ+  RI+LFY+G+L+ ++++Y W ++ ++ SPFV IF  +     A+ +NFV+L ++ S
Sbjct: 247 NQVVYRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLS 306

Query: 302 ALNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALL----FTSLLILFTPFISM 357
             NS ++S +R L+ LS   N    K  T+ S+ GVP+N+L+     TSL++L    +  
Sbjct: 307 VYNSGVYSNSRMLFGLSVQGNAP--KFLTRVSRRGVPINSLMLSGAITSLVVLINYLLP- 363

Query: 358 IPAISNSFVFITSVATNLFLVVYLMTLITYLKY-----RKSSDFDPKGFVLPAAHIFIPL 412
                 +F  + ++     L+ ++M  + +L++     R+  +   K  + P  + ++ +
Sbjct: 364 ----QKAFGLLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGN-YLCI 418

Query: 413 AIAGFVLIFISLFCFKDTI-VPAIGSVIWVLIFGLFTFFKKIK 454
           A  G +L+   L C  D + + AI   +W++   LF  FK ++
Sbjct: 419 AFLGMILL---LMCTMDDMRLSAILLPVWIVF--LFMAFKTLR 456


Lambda     K      H
   0.330    0.144    0.431 

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: 534
Number of extensions: 28
Number of successful extensions: 3
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: 457
Length of database: 458
Length adjustment: 33
Effective length of query: 424
Effective length of database: 425
Effective search space:   180200
Effective search space used:   180200
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