GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Escherichia coli BW25113

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)

Query= TCDB::P24207
         (458 letters)



>FitnessBrowser__Keio:1937132
          Length = 461

 Score =  392 bits (1006), Expect = e-113
 Identities = 193/440 (43%), Positives = 293/440 (66%), Gaps = 7/440 (1%)

Query: 13  SNQEPTLHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMR 72
           ++ +P L RGL  RHI+LIALGG IG GLF+G    ++ AGP+VLL Y +AG+  F IMR
Sbjct: 2   ADNKPELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMR 61

Query: 73  QLGEMVVEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPD 132
            +GEM+  EPV+GSFA +A++Y  PF G+L+ W+YW M++ VG++E+TA G+Y+Q+WFP+
Sbjct: 62  SMGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPE 121

Query: 133 VPTWIWAAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMIGFGLWLLF--SGHGGE 190
           +  WI A     ++   NL  VRLYGE EFWFA+IKV  II MI  GL ++F   G+GG+
Sbjct: 122 MAQWIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNGGQ 181

Query: 191 KASIDNLWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVV 250
                NL  +GGFFA GW G + +L +++ S+ G+ELIGITA EA++P+ ++  AV +V+
Sbjct: 182 SIGFSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVL 241

Query: 251 YRILLFYIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNS 310
           +RIL+FY+G++ V++ ++PW E+ SN SPFV+ F  +     A  +NFV+L A+LS  NS
Sbjct: 242 WRILIFYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNS 301

Query: 311 GVYSNSRMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLL--PQKAFG 368
           G+YS  RML+ L+     P  + +VSR GVP+  + +S AI  +   +NY++  PQ+ F 
Sbjct: 302 GMYSCGRMLYALAKNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYIIPNPQRVFV 361

Query: 369 LLMALVVATLLLNWIMICLAHLRFRAAMRRQGRETQFKALLYPFGNYLCIAFLGMILLLM 428
            + +  V   ++ W +I ++ LRFR A +       F+++L+P+ NY+ +AFL  +L+ M
Sbjct: 362 YVYSASVLPGMVPWFVILISQLRFRRAHKAAIASHPFRSILFPWANYVTMAFLICVLIGM 421

Query: 429 CTMDDMRLSAILLPVWIVFL 448
              +D R+S   L V I+F+
Sbjct: 422 YFNEDTRMS---LFVGIIFM 438


Lambda     K      H
   0.329    0.143    0.447 

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: 634
Number of extensions: 31
Number of successful extensions: 3
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: 458
Length of database: 461
Length adjustment: 33
Effective length of query: 425
Effective length of database: 428
Effective search space:   181900
Effective search space used:   181900
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