GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP in Cupriavidus basilensis 4G11

Align Serine permease SerP1 (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter

Query= SwissProt::A2RI87
         (459 letters)



>FitnessBrowser__Cup4G11:RR42_RS33495
          Length = 465

 Score =  289 bits (740), Expect = 1e-82
 Identities = 149/388 (38%), Positives = 237/388 (61%), Gaps = 13/388 (3%)

Query: 11  QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70
           +RGL+NRHIQLIA+ G IGTGLFLG  +TI+M GPSV+  Y + GI  FF +R +GEM+ 
Sbjct: 14  KRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMVV 73

Query: 71  NDPSQHSFLNFVTKYSGIRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPHLPLWLIE 130
           ++P   SF +F  KY G   G+ + W+YW++ + V ++EL+A+G Y+Q+W PH+P W   
Sbjct: 74  DEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWASA 133

Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAILGMIVTAIILVASNFHYTTVLSGKTVN 190
           +    L+  +N  + + FGE EFWF+++KV AI+GMIV    L+AS           T  
Sbjct: 134 LGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASG----------TAG 183

Query: 191 DTASLNNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250
             AS++N++     FP+G    V A+ ++MF+F  +E +G+TAAE   P+K++PKA NQ+
Sbjct: 184 PQASVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQV 243

Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVIVFQLIGIKWAAALINFVVLTSAASALN 310
             RIL+FYVGAL  +++++ W  +    SPFV++F  +     A ++N VVLT+A S  N
Sbjct: 244 IYRILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYN 303

Query: 311 SSLFSATRNMYSLAKQHDKGRLTAFTKLSKAGIPINALYMATALSLLAPVLTLIPQIKNA 370
           S ++  +R ++ LAKQ +  +  A  K++K GIP+ AL + +AL+  A V+        A
Sbjct: 304 SGVYCNSRMLFGLAKQGNAPK--ALLKVNKRGIPLAALGV-SALATAACVVINYFMPGEA 360

Query: 371 FNFAASCTTNLFLVVYFITLYTYWQYRK 398
           F        +  ++ + +    + ++R+
Sbjct: 361 FELLMGLVVSALIINWAMISIIHLKFRR 388


Lambda     K      H
   0.329    0.141    0.435 

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: 545
Number of extensions: 26
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: 465
Length adjustment: 33
Effective length of query: 426
Effective length of database: 432
Effective search space:   184032
Effective search space used:   184032
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