Alignments for a candidate for STP6 in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for STP6 in Clostridium tyrobutyricum FAM22553

Align The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized)
to candidate WP_039652874.1 PN53_RS08915 sugar porter family MFS transporter

Query= TCDB::Q9LT15
         (514 letters)



>NCBI__GCF_000816635.1:WP_039652874.1
          Length = 455

 Score =  238 bits (607), Expect = 3e-67
 Identities = 149/455 (32%), Positives = 245/455 (53%), Gaps = 33/455 (7%)

Query: 33  AMGGLLFGYDLGISGGVTSMEEFLTKFFPQVESQMKKAKHDTAYCKFDNQMLQLFTSSLY 92
           A GG +FGYD+GI  G     +      P +E  +                    TS L+
Sbjct: 15  AFGGFMFGYDIGIINGALPGIKTTWGISPLLEGWI--------------------TSGLF 54

Query: 93  LAALVASFMASVITRKHGRKVSMFIGGLAFLIGALFNAFAVNVSMLIIGRLLLGVGVGFA 152
           + A++ + + + +  + GR+  +    + F+IGAL +AF+ + S LI  R++LGV VG A
Sbjct: 55  VGAMIGASLMASLADRFGRRRMIMWSAIVFVIGALGSAFSTSTSFLIFARIILGVAVGGA 114

Query: 153 NQSTPVYLSEMAPAKIRGALNIGFQMAITIGILVANLINYGTSKMAQHGWRVSLGLAAVP 212
           +   P+Y+ E++PA+ RG L+   Q+ ITIG+L+A  INY    + + GWR  LG A VP
Sbjct: 115 SALVPMYMGEISPAEERGKLSGLNQLMITIGMLIAYGINYAFVHVFE-GWRWMLGGAMVP 173

Query: 213 AVVMVIGSFILPDTPNSMLERGKNEEAKQMLKKIRGADNVDHEFQDLIDAVEAAKKVENP 272
           A+V++ G+FILP++P  ++  GKNE A+++L+ +R +   + E+Q++I++  +       
Sbjct: 174 ALVLLFGTFILPESPRFLVRIGKNELARKVLQSMRSSKEAESEYQEIINSKYSD---SGS 230

Query: 273 WKNIMESKYRPALIFCSAIPFFQQITGINVIMFYAPVLFKTLGFGDDAALMSAVITGVVN 332
           +K++   K  PA++    +   QQI G N I +Y+  +   +   D   ++S V  GVV 
Sbjct: 231 FKDLFGKKALPAVVAGCGLTLLQQIQGANTIFYYSSQILAKVFGSDIGGVISTVGIGVVF 290

Query: 333 MLSTFVSIYAVDRYGRRLLFLEGGIQMFICQLLVGSFIGARFGTSGTGTLTPATADW-IL 391
           +L+T V++  VDR+ RR LF+ G I M +  LLVG                 A A W + 
Sbjct: 291 VLATVVTLMIVDRFKRRSLFMSGSIGMGVSLLLVGLIY-------PYAQANHAWAMWTVF 343

Query: 392 AFICVYVAGFAWSWGPLGWLVPSEICPLEIRPAGQAINVSVNMFFTFLIGQFFLTMLCHM 451
             ICVYV  +A+SW  + W+V  E+ P ++R     I  +VN F   L+  FF  +L  +
Sbjct: 344 ILICVYVIFYAYSWAAVTWIVVGELFPSQVRGIATGIASTVNWFGNILVALFFPVLLETV 403

Query: 452 KFGLFYF-FASMVAIMTVFIYFLLPETKGVPIEEM 485
              + +F FA++  +  +F  F+L ETKG  +EE+
Sbjct: 404 GLSMIFFGFAAICILGFLFAKFVLYETKGKSLEEI 438


Lambda     K      H
   0.327    0.141    0.434 

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: 632
Number of extensions: 45
Number of successful extensions: 6
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: 514
Length of database: 455
Length adjustment: 34
Effective length of query: 480
Effective length of database: 421
Effective search space:   202080
Effective search space used:   202080
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources