GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucP in Shewanella amazonensis SB2B

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)

Query= SwissProt::P11551
         (438 letters)



>FitnessBrowser__SB2B:6937233
          Length = 415

 Score =  244 bits (622), Expect = 5e-69
 Identities = 143/412 (34%), Positives = 218/412 (52%), Gaps = 23/412 (5%)

Query: 18  AGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFII 77
           A  + +Y      L +LFF+W     LNDIL+P  +  F+L   QA LIQ  F+  YF++
Sbjct: 14  AAGAENYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLV 73

Query: 78  PIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETA 137
            +PAG+L+K+L Y+ GI+ GL   ALG  LF+PAA    Y +FL  LF++A+G+  L+ A
Sbjct: 74  SVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVA 133

Query: 138 ANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQL 197
           ANP+VT LGP  +   RL L Q FNS G  IA  FG  LILS                 +
Sbjct: 134 ANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILS---------------VAV 178

Query: 198 SAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARI 257
            A   +   +V+ PY+++  +++++A++  L K P +       A  G      S LA  
Sbjct: 179 GASAEAEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ-----SALAH- 232

Query: 258 RHWRWAVLAQFCYVGAQTACWSYLIRYAVE-EIPGMTAGFAANYLTGTMVCFFIGRFTGT 316
           RH     +  F YVG + A  S+L+ +  E  + GM    AA+Y+        +GRF G 
Sbjct: 233 RHLVLGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGA 292

Query: 317 WLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNL 376
            ++ +    KVL   A +A  L L++  + G + + A+     F SI +PTIFSL +KNL
Sbjct: 293 AVMQKVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNL 352

Query: 377 GQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428
           G  T  GS  + + I+GG +V  + G ++D+ G +  + ++P LC+  I  +
Sbjct: 353 GPATAQGSGILCLAIVGGALVPLLQGLLADSVG-LSASFILPVLCYGYILFY 403


Lambda     K      H
   0.329    0.140    0.425 

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: 471
Number of extensions: 33
Number of successful extensions: 5
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: 415
Length adjustment: 32
Effective length of query: 406
Effective length of database: 383
Effective search space:   155498
Effective search space used:   155498
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