GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP1 in Pseudomonas stutzeri RCH2

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 GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases

Query= TCDB::F2HQ25
         (459 letters)



>FitnessBrowser__psRCH2:GFF1660
          Length = 464

 Score =  297 bits (761), Expect = 4e-85
 Identities = 159/399 (39%), Positives = 240/399 (60%), Gaps = 24/399 (6%)

Query: 11  QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70
           QRGL+NRHIQLIA+ G IGTGLFLG+   ++  GPS+I  Y + G   F  +R +GEM+ 
Sbjct: 12  QRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMIV 71

Query: 71  NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130
            +P   SF +F  KY G   G+ + W+YW++ V V ++ELTA+G Y+QFW P+VP W   
Sbjct: 72  EEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWATA 131

Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190
                L+  +N  N + FGETEFWFA++KVAAI+GMI+  + L         ++SGK   
Sbjct: 132 AAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFL---------LVSGKG-G 181

Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250
           + AS+SN++     FP+G    + AL ++MF+F  +E +G+TAAE   PK  +PKAINQ+
Sbjct: 182 EQASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQV 241

Query: 251 PVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKWAAALINFVV 301
             RIL+FY+GAL  ++A++ W  +         P   SPFV +F LIG   AA L+NFVV
Sbjct: 242 VYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVV 301

Query: 302 LTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVL 361
           LT+A S  NS ++  +R +Y LA+Q D  R     K++  G+P+ A+ ++  ++LL   +
Sbjct: 302 LTAALSVYNSGVYCNSRMLYGLAEQGDAPR--SLMKINSRGVPVLAVGVSALVTLLCVAV 359

Query: 362 T-LIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKS 399
             L PQ   A +   S      ++ + +    + ++R++
Sbjct: 360 NYLFPQ--GALELLMSLAVAALVINWAMISLAHLKFRRA 396


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: 604
Number of extensions: 33
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: 464
Length adjustment: 33
Effective length of query: 426
Effective length of database: 431
Effective search space:   183606
Effective search space used:   183606
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