GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fucP in Klebsiella michiganensis M5al

Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter

Query= SwissProt::P11551
         (438 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS22920 BWI76_RS22920 MFS
           transporter
          Length = 436

 Score =  817 bits (2110), Expect = 0.0
 Identities = 406/438 (92%), Positives = 425/438 (97%), Gaps = 2/438 (0%)

Query: 1   MGNTSIQTQSYRAVDKDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN 60
           MGNT+IQTQS+RAV+   G+S+ YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN
Sbjct: 1   MGNTTIQTQSFRAVE--TGKSKRYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN 58

Query: 61  FQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLF 120
           FQAGLIQSAFYFGYF+IPIPAGILMKKLSYKAGIITGLFLYA GAALFWPAAE+MNYTLF
Sbjct: 59  FQAGLIQSAFYFGYFVIPIPAGILMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLF 118

Query: 121 LVGLFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSN 180
           L+GLFIIAAGLGCLETAANPFVTVLGPES GHFRLNLAQTFNSFGAIIAVVFGQSLILSN
Sbjct: 119 LIGLFIIAAGLGCLETAANPFVTVLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSN 178

Query: 181 VPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHS 240
           VPHQSQDVLDKM+PEQLSAYKHSLVLSVQTPYMIIVA+VLLVALLIMLTKFPALQSD+HS
Sbjct: 179 VPHQSQDVLDKMAPEQLSAYKHSLVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHS 238

Query: 241 DAKQGSFSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANY 300
           DA Q SFSASL+RL R+RHWRWAVLAQFCYVGAQTACWSYLIRYA+EEIPGMT GFAANY
Sbjct: 239 DATQSSFSASLARLVRVRHWRWAVLAQFCYVGAQTACWSYLIRYAIEEIPGMTPGFAANY 298

Query: 301 LTGTMVCFFIGRFTGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAF 360
           LTGTMVCFFIGRF+GTWLISRFAPHKVLAAYAL++M LCLISAF GGHVGL+ALTLCSAF
Sbjct: 299 LTGTMVCFFIGRFSGTWLISRFAPHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAF 358

Query: 361 MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPAL 420
           MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAEL+PAL
Sbjct: 359 MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPAL 418

Query: 421 CFAVIFIFARFRSQTATN 438
           CFAVIFIFARFRSQTA N
Sbjct: 419 CFAVIFIFARFRSQTAAN 436


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: 800
Number of extensions: 10
Number of successful extensions: 2
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: 436
Length adjustment: 32
Effective length of query: 406
Effective length of database: 404
Effective search space:   164024
Effective search space used:   164024
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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