GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlE in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-mannitol and D-mannose, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_5038 Various polyols ABC transporter, periplasmic substrate-binding protein

Query= reanno::pseudo3_N2E3:AO353_25880
         (436 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5038 Various polyols ABC
           transporter, periplasmic substrate-binding protein
          Length = 436

 Score =  676 bits (1744), Expect = 0.0
 Identities = 321/423 (75%), Positives = 372/423 (87%), Gaps = 2/423 (0%)

Query: 16  LSSVSL--GAQTLTIATVNNSDMIRMQKLSKTFEAEHPEIKLNWVVLEENVLRQRLTTDI 73
           LSS  L   A+T+TIATVNNSDMIRMQ+LSKTFE +HP++KLNWVVLEENVLRQRLTTDI
Sbjct: 14  LSSALLCQAAETVTIATVNNSDMIRMQRLSKTFEQQHPDVKLNWVVLEENVLRQRLTTDI 73

Query: 74  ATQGGQFDVLTIGMYEAALWGAKGWLEPMKDLPAGYALDDVFPSVREGLSVKGTLYALPF 133
           ATQGGQFDVLTIG YE  LWGAK WLEPMKDLPA Y L+D+FPSVR+GLSV  TLYALPF
Sbjct: 74  ATQGGQFDVLTIGTYETPLWGAKHWLEPMKDLPASYDLEDIFPSVRQGLSVNDTLYALPF 133

Query: 134 YAESSMTYYRTDLFKDAGLAMPEHPTWEQIGEFAGKLNKPDQEQYGICLRGKAGWGENMA 193
           Y ES++TYYRTDLFK+AGL+MPEHPTW Q+GEFAGKL++PD+EQYG+CLRGKAGWGENMA
Sbjct: 134 YGESTITYYRTDLFKNAGLSMPEHPTWTQLGEFAGKLHQPDKEQYGMCLRGKAGWGENMA 193

Query: 194 LITTIANAYGARWFDEKWQPEFSGPEWKNALSFYADTMKKSGPPGASSNGFNENLALFNS 253
           L+TT++NA+GARWF+E+WQP+ +GPEW  A +FY +T+K+ GPPG SSNGFNE LALFNS
Sbjct: 194 LLTTMSNAFGARWFNEQWQPQLTGPEWTAAANFYVNTLKQYGPPGVSSNGFNETLALFNS 253

Query: 254 GKCAIWVDASVAGSFVTDKTQSKVSEHVGFTYAPHQVTDKGSAWLYSWALAIPTSSKAKD 313
           GKCAIWVDASVAGSF+TD TQSKV++ VGF  AP QVTDKGS+WLY+W+LAIP +SK K+
Sbjct: 254 GKCAIWVDASVAGSFITDTTQSKVADKVGFVAAPTQVTDKGSSWLYAWSLAIPATSKHKE 313

Query: 314 AAKTFSAWATSKEYGALVAEKDGIANVPPGTRASTYSEAYMNAAPFAKVTLESLKVADPG 373
           AAK F  WATSK+Y  LVA+KDGI NVPPGTR STYS AY+ AAPFA VTL+ ++ ADP 
Sbjct: 314 AAKAFVTWATSKDYIQLVADKDGITNVPPGTRMSTYSNAYLQAAPFASVTLKMMQHADPA 373

Query: 374 KPTLKPVPYIGIQLVTIPEFQAVGTQVGKLFSAALIGQTTVDQALAAAQQTTEREMKRAG 433
            P+++PVPY+GIQ VTIPEFQA+GT VGKL SAAL GQ  V+QALA+AQQTTEREMKRAG
Sbjct: 374 HPSVQPVPYVGIQYVTIPEFQAIGTSVGKLLSAALTGQMPVEQALASAQQTTEREMKRAG 433

Query: 434 YPK 436
           YPK
Sbjct: 434 YPK 436


Lambda     K      H
   0.315    0.130    0.391 

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: 700
Number of extensions: 10
Number of successful extensions: 1
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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