GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Escherichia coli BW25113

Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate 16885 b2801 L-fucose transporter (NCBI)

Query= TCDB::O25788
         (407 letters)



>lcl|FitnessBrowser__Keio:16885 b2801 L-fucose transporter (NCBI)
          Length = 438

 Score =  236 bits (601), Expect = 1e-66
 Identities = 148/415 (35%), Positives = 218/415 (52%), Gaps = 24/415 (5%)

Query: 2   QKTSNTLALGSLTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGG 61
           Q  S  +    L +LFFL      LNDIL+P  +  F LT F+A LIQ  F+  YFI+  
Sbjct: 20  QSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPI 79

Query: 62  VFGNVISKIGYPFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGN 121
             G ++ K+ Y  G++ G  + A G ALF+PAA   +Y  FL  LFI+A+G+ CL+TA N
Sbjct: 80  PAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAAN 139

Query: 122 PFVTLLSKGKEAR-NLVLVQAFNSLGTTLGPIFGSLLIFSTTKMGDNASLIDKLADAK-- 178
           PFVT+L         L L Q FNS G  +  +FG  LI S      +  ++DK++  +  
Sbjct: 140 PFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVP-HQSQDVLDKMSPEQLS 198

Query: 179 --------SVQMPYLGLAVFSLLLALIMYLLKLPDVEKEMPKETTQKS-------LFSHK 223
                   SVQ PY+ +    LL+AL++ L K P ++ +   +  Q S       L   +
Sbjct: 199 AYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGSFSASLSRLARIR 258

Query: 224 HFVFGALGIFFYVGGEVAIGSFLV-LSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVL 282
           H+ +  L  F YVG + A  S+L+  + E++  + +  +A+YL        +GRF G+ L
Sbjct: 259 HWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWL 318

Query: 283 MNKIAPNKYLAFNALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGH 342
           +++ AP+K LA  AL ++ L  ++   GG + L ALT    F SI +PTIFSL   NLG 
Sbjct: 319 ISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQ 378

Query: 343 LTSKASGVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLLCYFYILFFA 397
            T   S  I M I+GG ++ P+ G V+D       N+  A  +P LC+  I  FA
Sbjct: 379 DTKYGSSFIVMTIIGGGIVTPVMGFVSD----AAGNIPTAELIPALCFAVIFIFA 429


Lambda     K      H
   0.328    0.144    0.423 

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: 472
Number of extensions: 27
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: 407
Length of database: 438
Length adjustment: 32
Effective length of query: 375
Effective length of database: 406
Effective search space:   152250
Effective search space used:   152250
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 (21.7 bits)
S2: 50 (23.9 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