GapMind for catabolism of small carbon sources

 

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

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 N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= TCDB::F2HQ24
         (457 letters)



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

 Score =  300 bits (769), Expect = 5e-86
 Identities = 167/442 (37%), Positives = 261/442 (59%), Gaps = 10/442 (2%)

Query: 7   EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66
           + N   QRGL+ RHI+L+A+   IG GLFLG+  +I L GP+I+  YL+ G  ++I++RA
Sbjct: 2   QTNDSLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRA 61

Query: 67  IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126
           +GEM  Q+P   SF  +   YLG  PGY   W+Y  + +   +AE+ A+G Y+  W PD+
Sbjct: 62  LGEMAVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDV 121

Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLIL-TAIILIFSHYHTGTD 185
           P W+  +  LV +  +N    K +GE EFWF MIK+V I+ +I+    +++F   + G  
Sbjct: 122 PQWIWALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVP 181

Query: 186 TVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIP 245
           T  ++N+     F PNG      + QMVMFA++ +E IG+TA E DNP+ ++  AIN + 
Sbjct: 182 T-GISNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVF 240

Query: 246 IRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNS 305
            RI++FYVGAL  IMSIY W ++    SPFV  F+ +GIK AA ++NFVVLT+A S+ N 
Sbjct: 241 WRILIFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNG 300

Query: 306 ALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAISNS 364
            ++S  R L++L++    +  + F   S +G+P  A+L + + +LF   ++ ++PA    
Sbjct: 301 GIYSTGRMLFNLAQ--QGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPA--KV 356

Query: 365 FVFITSVATNLFLVVYLMTLITYLKYRKSSDFDPKG---FVLPAAHIFIPLAIAGFVLIF 421
           FV++TS AT   +  + + LIT +KYR+      +    F +P       LA+A  VL+ 
Sbjct: 357 FVWVTSAATFGAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVV 416

Query: 422 ISLFCFKDTIVPAIGSVIWVLI 443
             +  F DT V  I   +W+++
Sbjct: 417 GLMGYFPDTRVALIVGPLWLVL 438


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: 556
Number of extensions: 27
Number of successful extensions: 4
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: 454
Length adjustment: 33
Effective length of query: 424
Effective length of database: 421
Effective search space:   178504
Effective search space used:   178504
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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