GapMind for catabolism of small carbon sources

 

Aligments for a candidate for serP1 in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5633 Aromatic amino acid transport protein AroP

Query= TCDB::F2HQ25
         (459 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5633 Aromatic amino acid
           transport protein AroP
          Length = 472

 Score =  283 bits (724), Expect = 9e-81
 Identities = 150/401 (37%), Positives = 241/401 (60%), Gaps = 26/401 (6%)

Query: 9   EAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEM 68
           E +RGL+NRHIQLIA+ G IGTGLFLG+   ++  GPS+I  Y + G   F  +R +GEM
Sbjct: 10  ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69

Query: 69  LYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWL 128
           +  +P   SF +F  KY G   G+ + W+ W++ + V +SELTA+G YI +W P +P W+
Sbjct: 70  IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129

Query: 129 IEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMI-VTAIILVAGNFHYSTVLSGK 187
                  L+  +N  N + FGE EFWFA+IKV AI+GMI + + +LV+G+          
Sbjct: 130 SAAAFFILINVINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGH---------- 179

Query: 188 TVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAI 247
                AS++N++     FP+G    V A+ ++MF+F  +E +G TAAE   PK  +PKAI
Sbjct: 180 -GGPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAI 238

Query: 248 NQIPVRILLFYVGALLAIMAIFNWHYIPA---------DKSPFVMVFQLIGIKWAAALIN 298
           NQ+  RIL+FY+GAL+ ++++  W  + +           SPFV VF ++G   AA ++N
Sbjct: 239 NQVIYRILIFYIGALVVLLSLTPWDSLLSTLNASGDAYSGSPFVQVFSMLGSNTAAHILN 298

Query: 299 FVVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLA 358
           FVVLT+A S  NS  +  +R +  +A+Q D  ++   +K+ K G+P+ ++  + A++L+A
Sbjct: 299 FVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKV--LSKIDKRGVPVRSILASAAVTLVA 356

Query: 359 PVLT-LIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRK 398
            +L  LIPQ  +A +   S      ++ + +  Y+++++R+
Sbjct: 357 VLLNYLIPQ--HALELLMSLVVATLVINWAMISYSHFKFRQ 395


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: 601
Number of extensions: 38
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: 459
Length of database: 472
Length adjustment: 33
Effective length of query: 426
Effective length of database: 439
Effective search space:   187014
Effective search space used:   187014
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 (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