GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuE in Pseudomonas fluorescens FW300-N2E3

Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate AO353_25115 AO353_25115 ABC transporter substrate-binding protein

Query= TCDB::Q9R9Q7
         (423 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25115
          Length = 424

 Score =  364 bits (935), Expect = e-105
 Identities = 183/421 (43%), Positives = 269/421 (63%), Gaps = 4/421 (0%)

Query: 7   VRTLISCAAI---AGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMP 63
           ++TL+  A +   AG   +++AA+L+++  + G  L   ++ +  + K+TG+ V +V+ P
Sbjct: 4   LKTLLPAALLTLFAGLPSVSSAADLTISCGAVGAELQLCKEAVEAWSKQTGNNVEVVSTP 63

Query: 64  ASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATK-DVVGEHFPSIIQS 122
            S++E+ S Y+  L+A + D+D+ Q D++W   LA+  +DL E    +    +F + + +
Sbjct: 64  NSATERLSFYQQILSAQSTDIDIIQIDMVWPGMLAKHLMDLREVLPANATQGYFQAQVDN 123

Query: 123 QTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIW 182
            TVNG+LV +P++TD+  LYYRKDLL+KY K  P+TW+E+ ATA++VQ  ER AG+ D+W
Sbjct: 124 ATVNGRLVTMPWFTDSGLLYYRKDLLEKYNKQVPQTWEEMTATARDVQQAERNAGNPDVW 183

Query: 183 GFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKG 242
           G++FQG AYEGLTCNALEWI S   G ++ P G I VN++ + AA+   K W+G I+P+G
Sbjct: 184 GYIFQGRAYEGLTCNALEWISSQPEGGLVNPRGDIVVNSQASRAALTLAKSWVGDISPRG 243

Query: 243 VLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTL 302
           VL Y EEE RGV+Q+GNA+FMRNWPY +AL    +SAVK K  VAPLP   +    +STL
Sbjct: 244 VLNYTEEEGRGVFQSGNALFMRNWPYVWALVQSQNSAVKDKVGVAPLPRGGETGNHASTL 303

Query: 303 GGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMP 362
           GGW LAVS+YS   + A   V +L SA+ QK RA+  +  P I +LY DPE+ AA P+  
Sbjct: 304 GGWGLAVSRYSAHPKLAADLVSYLTSAQQQKHRALIGAYNPVIESLYQDPELLAAMPYYG 363

Query: 363 HWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKGDA 422
               I    V RP+++   +Y  VS+ F+  VH  L+G     + L  LE ELT +K   
Sbjct: 364 QLHSILNDGVMRPASITADRYPRVSNAFFDRVHGVLAGELPVDQALAELESELTRIKRRN 423

Query: 423 W 423
           W
Sbjct: 424 W 424


Lambda     K      H
   0.313    0.129    0.383 

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: 459
Number of extensions: 18
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: 423
Length of database: 424
Length adjustment: 32
Effective length of query: 391
Effective length of database: 392
Effective search space:   153272
Effective search space used:   153272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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