GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Chryseobacterium viscerum 687B-08

Align MFS transporter (characterized, see rationale)
to candidate WP_103231791.1 C1634_RS07405 MFS transporter

Query= uniprot:A0A1X9ZCC9
         (458 letters)



>NCBI__GCF_002899945.2:WP_103231791.1
          Length = 472

 Score =  339 bits (870), Expect = 1e-97
 Identities = 181/447 (40%), Positives = 276/447 (61%), Gaps = 16/447 (3%)

Query: 8   ENPKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQ 67
           + P L+++QIINMS+GF GIQ  + LQ  N  RI  NLGA+  ++   +L AP+TGL+VQ
Sbjct: 17  KKPNLSMLQIINMSMGFLGIQMAFGLQNGNASRILGNLGADVHELSWFWLVAPVTGLIVQ 76

Query: 68  PIIGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHSS---------VLWMAAGLLWI 118
           PIIG++ D TW P  GRR+PYF+IGA++ ++ L+ +P+++          L +A   L +
Sbjct: 77  PIIGHMGDNTWSPL-GRRKPYFLIGAVLCAVGLVLLPNAASVTQMFAANALLLAVIFLAM 135

Query: 119 LDVFGNIAMEPFRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALP-WIMNNVFHLTNT 177
           +D   NIAMEPFRA V D LP  Q   GF +Q+++IG+G  + S LP W+      ++N 
Sbjct: 136 MDASVNIAMEPFRALVGDMLPKHQGTIGFSVQTILIGIGAVLGSYLPDWLTK--IGISNE 193

Query: 178 AEQGSIPENVKFSFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREI 237
           A QG + +NV +SFYIGA     ++L+T+ TT+EY PQ+    E  KE+ K       +I
Sbjct: 194 APQGFVADNVIYSFYIGAGLLIISILYTIMTTREYSPQEFAEFEDEKEAEK-HESKFSDI 252

Query: 238 FHALRNMPKRMQIVSLVQFFTWPGLFLMWFYYTTAVAVNVFG--GKDAADPVYAQGADFG 295
           F    ++P +M+ + +VQFF+W  LF MW + T+A+A +  G   +D     +    D  
Sbjct: 253 FKDFASIPVQMKKLGIVQFFSWFALFTMWVFTTSALATHHLGLSPEDTHSKAFNDAGDLT 312

Query: 296 SLTLAYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISVAWVHDKNMLYLCMTG 355
                 Y++    FA +L  IA  +G+K THAL L+CG +GLIS+ ++ + + L++ M G
Sbjct: 313 GKLFGMYNLWAIPFAFLLTPIAKLIGKKQTHALALLCGGLGLISMYFIKEVDHLWISMIG 372

Query: 356 VGIAWASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRL 415
           +G AWASIL+MPYAML   +P+ K+G+YMGIFNFFIV+P+II  L  G ++  +     +
Sbjct: 373 LGFAWASILAMPYAMLIDVIPQRKMGVYMGIFNFFIVIPQIINGLFGGPIVSGIFGKQAM 432

Query: 416 LAVQLGGGLMILAAVICYVFIREPKKT 442
             V +GG  M++ AV+  +F++   +T
Sbjct: 433 DYVVVGGVCMLIGAVVTMIFVKSEDET 459


Lambda     K      H
   0.327    0.142    0.448 

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: 674
Number of extensions: 42
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: 458
Length of database: 472
Length adjustment: 33
Effective length of query: 425
Effective length of database: 439
Effective search space:   186575
Effective search space used:   186575
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: 51 (24.3 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