GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Hafnia paralvei ATCC 29927

Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate WP_008815659.1 M988_RS00265 sn-glycerol-3-phosphate ABC transporter permease UgpA

Query= SwissProt::O51924
         (295 letters)



>NCBI__GCF_001655005.1:WP_008815659.1
          Length = 295

 Score =  139 bits (349), Expect = 1e-37
 Identities = 86/283 (30%), Positives = 142/283 (50%), Gaps = 9/283 (3%)

Query: 11  YREAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSARE 70
           ++ + L Y ++ P L +  +F + P     W S+     F     FVG +N++ +     
Sbjct: 8   FKRSWLPYALVAPQLLITAIFFLWPAGEALWYSVQSLDPFGLSSEFVGWQNFITLWHDPY 67

Query: 71  FWYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWE 130
           +  +   T+ FS +      +L L FA ++N  L+GR   + + ++P+AV   I+A  W 
Sbjct: 68  YLSAFRTTLWFSGLVTFFGLVLSLFFAALVNHILRGRRFYQTLFILPYAVAPTIAAVLWM 127

Query: 131 LMYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAIPQ 190
            ++N   GL +  L ++G S  N       A F +V+A VWK   +  L  LA LQ++P+
Sbjct: 128 FLFNPGLGLVSHFLGVMGYS-WNHAQNSGQAMFLVVLASVWKQVSYNFLFFLAALQSVPK 186

Query: 191 DLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDA-LRVFDIIYVLTGGGPGGAT 249
            L EAA IDGA    RF  I LPL+ PV    L++  + A    F +I   TGGGPG +T
Sbjct: 187 SLLEAAAIDGAGPIRRFFHIVLPLISPVSFFLLVVNLVYAFFDTFPVIDAATGGGPGQST 246

Query: 250 TSISLLAFNYYNLG----DYGIGSAISILTFVLVLSFTIVYLK 288
           T+   L +  Y  G    D    +A S++  ++V++ T++  +
Sbjct: 247 TT---LIYKIYREGFAGLDLSSSAAQSVVLMLIVVALTMIQFR 286


Lambda     K      H
   0.329    0.145    0.439 

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: 237
Number of extensions: 18
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: 295
Length of database: 295
Length adjustment: 26
Effective length of query: 269
Effective length of database: 269
Effective search space:    72361
Effective search space used:    72361
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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