GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N2E2

Align Amino acid permease (characterized, see rationale)
to candidate Pf6N2E2_4959 S-methylmethionine permease

Query= uniprot:A0A0N9WG97
         (470 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959
          Length = 476

 Score =  310 bits (794), Expect = 7e-89
 Identities = 164/454 (36%), Positives = 265/454 (58%), Gaps = 9/454 (1%)

Query: 12  NREHGLRRQLTSGQMSMIAIGGAIGTGLFMGSAYAIGYAGP-SVLLSYAIGAVITLLLMG 70
           N   G ++++ +  + M+A+GG IGTGLF+ S Y +  AGP   +++Y IGA++  ++M 
Sbjct: 9   NTRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMM 68

Query: 71  CLAEMTVAHSTSGSFGAYAEFYISPLAGFLVRYAYWAAIVLAVGTEVTAVAMYMKYWFAN 130
           CL E+ V    +GSF  YA  ++ P  G+ V + YW    +A+G+E TA  + M  WF +
Sbjct: 69  CLGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPD 128

Query: 131 VPEWIWIVSFSSILIVLNAISVKTFGTFEYWFSTIKIGAIVGFIILAVYVVFGSGNPEY- 189
            P WIW   F+ ++ + N ISV+ F   E+W S IK+  +V F+++    + G  N +  
Sbjct: 129 TPVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQA 188

Query: 190 ---GVHHYTSHGGFFPNGLQGMWVAVIVSIFSYLSVEMIAVAAGEAEDPERAVKKAFRAT 246
              G+ ++T  G  FP G   + + ++   F++   E+I +AAGE +DP+R V +A R T
Sbjct: 189 HSIGLSNFTREG-LFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTT 247

Query: 247 IVRLVVFYLLTLALMLAIVPWVQAGHAQSPFVTVMQTIGIPGATGVMNFVILIAALSAMN 306
           ++RL VF++ T+ ++  ++P  QAG  +SPFVTV   IGIP +  +MNFVI+ A LSA N
Sbjct: 248 VLRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSAAN 307

Query: 307 SQLYITTRMMFSLSRGGYAPKAMGALSKSGIPLNALLLSSSGIALATLLNVMYPESSFTL 366
           S LY  +RM+++LS  G+ PK   AL++ G PLNA+++S +G A + L +V   ++ +  
Sbjct: 308 SGLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIYLA 367

Query: 367 MMAISMFGAIFTWFMIFLTHYCFRRYHQRHGE--RKLSFRMRLFPYTTLLGLVLMGAVMI 424
           +++IS    +  W  I  +   FRR++  +G   RKL FR+R +P+  L  LV      I
Sbjct: 368 LVSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSLACI 427

Query: 425 TTYFTEAFKMTLVFGVPFLLILSLVYGVFFRKTR 458
              F    ++ L FG+PF+     VY +  RK+R
Sbjct: 428 GIAFDPEQRVALYFGLPFIAWCYFVYYI-TRKSR 460


Lambda     K      H
   0.328    0.140    0.422 

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: 648
Number of extensions: 37
Number of successful extensions: 4
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: 470
Length of database: 476
Length adjustment: 33
Effective length of query: 437
Effective length of database: 443
Effective search space:   193591
Effective search space used:   193591
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