GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Escherichia coli BW25113

Align L-tyrosine transporter (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)

Query= reanno::pseudo5_N2C3_1:AO356_18530
         (471 letters)



>lcl|FitnessBrowser__Keio:1937132 b3795 predicted transporter (NCBI)
          Length = 461

 Score =  361 bits (927), Expect = e-104
 Identities = 180/444 (40%), Positives = 278/444 (62%), Gaps = 16/444 (3%)

Query: 10  ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEM 69
           EL+RGL+ RHI+LIALGG IG GLF+G+A  LK AGPS++L Y I G   F IMR +GEM
Sbjct: 7   ELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMGEM 66

Query: 70  IVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTWV 129
           +  EPV GSF+ +AH+Y   F G+L+ W+ W +++ VG+SE+TA+G Y+ +W P++  W+
Sbjct: 67  LFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQWI 126

Query: 130 SAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLV--SGHGGPQASVT 187
            A     L+   NLA V+++GE EFWFA+IKV  I+ MI +G  ++    G+GG     +
Sbjct: 127 PALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQSIGFS 186

Query: 188 NLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQVIYRILI 247
           NL  HGGFF  G  G + A+ I++ S+ G+E++G TA EA  P+  +  A+ +V++RILI
Sbjct: 187 NLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLWRILI 246

Query: 248 FYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFVVLTAALS 307
           FY+GA+ V++++ PW+ +           +GSPFV  F+ +G   AA I+NFVVLTAALS
Sbjct: 247 FYVGAIFVIVTIFPWNEI---------GSNGSPFVLTFAKIGITAAAGIINFVVLTAALS 297

Query: 308 VYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLNYLV--PQ 365
             NSG Y   RML  +A+    P A++++ + GVPV  +  S A+ L+   LNY++  PQ
Sbjct: 298 GCNSGMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQ 357

Query: 366 HALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALWYPYGNYICLAFVVFI 425
                + S  V   ++ W +I  S  +FR+       +  F+++ +P+ NY+ +AF++ +
Sbjct: 358 RVFVYVYSASVLPGMVPWFVILISQLRFRRAHKAAIASHPFRSILFPWANYVTMAFLICV 417

Query: 426 LGVMLLIPGIQISVYAIPVWVVFM 449
           L  M      ++S++   V ++FM
Sbjct: 418 LIGMYFNEDTRMSLF---VGIIFM 438


Lambda     K      H
   0.327    0.139    0.432 

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: 628
Number of extensions: 31
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 471
Length of database: 461
Length adjustment: 33
Effective length of query: 438
Effective length of database: 428
Effective search space:   187464
Effective search space used:   187464
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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