GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoP in Shewanella amazonensis SB2B

Align 2-Deoxy-D-ribose porter, DeoP (characterized)
to candidate 6936374 Sama_0562 glucose/galactose transporter (RefSeq)

Query= TCDB::Q8XEV7
         (438 letters)



>FitnessBrowser__SB2B:6936374
          Length = 413

 Score =  194 bits (492), Expect = 6e-54
 Identities = 128/415 (30%), Positives = 203/415 (48%), Gaps = 30/415 (7%)

Query: 22  FILLSCLFPLWGCAAALNDILITQFKSVFSLSNFASALVQSAFYGGYFLIAIPASLVIKK 81
           F  ++ LF +WG   ALNDILI   K +F LS   + LVQ  F+G YFL++  A ++I +
Sbjct: 25  FGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIAR 84

Query: 82  TSYKVAILIGLTLYIVGCTLFFPASHMATYTMFLAAIFAIAIGLSFLETAANTYSSMIGP 141
             Y   I+ GL+    GC LF+PAS +  Y +FL A+F +A G++ L+ +AN + + +GP
Sbjct: 85  IGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGP 144

Query: 142 KAYATLRLNISQTFYPIGAAAGILLGKYLVFSEGESLEKQMAGMNAEQVHNFKVLMLENT 201
           +  A  RLN++Q    +G   G L G  L+F          AG +            E  
Sbjct: 145 ERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAA-------AGTH------------EAV 185

Query: 202 LEPYKYMIMVLVVVMVLFLLTRFPTCKVAQTASHKRPSALDTLRYLASNARFRRGIVAQF 261
             PY  +  V+ ++ V F+              H+   +      L S+ R   G +A F
Sbjct: 186 QLPYLLLAAVIGIIAVGFIFLGGKVKHADMGVDHRHKGS------LLSHKRLLLGALAIF 239

Query: 262 LYVGMQVAVWSFTIRLALE--LGDINERDASTFMVYSFACFFIGKFIANILMTRFNPEKV 319
           LYVG +V++ SF +    E  +G ++E+ A+  + + +    IG+F    L  RFNP  V
Sbjct: 240 LYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMV 299

Query: 320 LILYSVIGALFLAYVALAPSFSAVYVAVLVSVLFGPCWATIYAGTLDTVDNEHTEMAGAV 379
           L   +V   L L    ++    A+   + V       + TI+   ++ +  E T     +
Sbjct: 300 LAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGL-GELTSRGSGL 358

Query: 380 IVMAIVGAAVVPAIQGYVADMFHSLQLSFLVSMLCFVYVGVY-FWRESKVRGNLA 433
           +  AIVG A++P IQG VAD    +QLSF+V   C+ Y+  Y F+  +++ G  A
Sbjct: 359 LCQAIVGGALLPVIQGVVADNV-GVQLSFIVPTFCYFYICWYAFFARNRMNGETA 412


Lambda     K      H
   0.329    0.139    0.412 

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: 382
Number of extensions: 16
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: 438
Length of database: 413
Length adjustment: 32
Effective length of query: 406
Effective length of database: 381
Effective search space:   154686
Effective search space used:   154686
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