GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Sporolactobacillus vineae SL153

Align MFS transporter (characterized, see rationale)
to candidate WP_010632377.1 RH97_RS10790 SLC45 family MFS transporter

Query= uniprot:A0A1X9ZCC9
         (458 letters)



>NCBI__GCF_000246965.1:WP_010632377.1
          Length = 459

 Score =  233 bits (595), Expect = 8e-66
 Identities = 133/450 (29%), Positives = 234/450 (52%), Gaps = 15/450 (3%)

Query: 10  PKLTLVQIINMSVGFFGIQFGWDLQRANMGRIYENLGANPDQVPLLFLAAPLTGLLVQPI 69
           P+L+L+ I  M+ GFFG+   + LQ + MGRI++ +GA+P ++   F+  PL G++VQP+
Sbjct: 11  PRLSLMTIFAMTFGFFGVNMAFSLQFSQMGRIFQTIGADPTRLGYFFILPPLAGMIVQPL 70

Query: 70  IGYLSDRTWHPKWGRRRPYFMIGAIVSSIALIFMPHS----------SVLWMAAGLLWIL 119
           +G  SD TW  K GRR PY +IGA ++++ +I +P+S          + L   A  +  +
Sbjct: 71  VGKYSDLTWSNKLGRRMPYLLIGAPIAALVMILLPNSGSFGFGYASFAALLFGAVAILFM 130

Query: 120 DVFGNIAMEPFRAFVTDKLPDSQVNRGFIMQSMMIGLGGSVASALPWIMNNVFHLTNTAE 179
           D+  N+ M+PF+  + D + + Q +  +  Q     LGG +A+ +P+++  VF + NTA 
Sbjct: 131 DLSSNVCMQPFKMIIGDMVNEKQKDLAWSWQQSFSNLGGVIATIIPFVL-TVFGVANTAP 189

Query: 180 QGSIPENVKFSFYIGAFFFFAAVLWTVFTTKEYPPQDVDFKEKVKESNKGFGGGAREIFH 239
           +G +P +V+ +FY+GA       L+T+ + KEY P+       +K         +  ++H
Sbjct: 190 RGEVPLSVRLAFYVGAGVLLLTSLYTIISVKEYDPKTYALYHHMKADEH---KDSPSLWH 246

Query: 240 ALRNMPKRMQIVSLVQFFTWPGLFLMWFYYTTAVAVNVFGGKDAADPVYAQGADFGSLTL 299
            +R  P+    VSLVQ F W     +W Y T A+A NV+G  D A   Y    ++  +  
Sbjct: 247 LVRKAPRAFWEVSLVQLFDWFAFQYLWTYATGAIAQNVWGTADPASAGYQAAGNWYGILT 306

Query: 300 AYYSVITFLFALVLPKIADALGRKTTHALCLICGAIGLISVAWVHDKNMLYLCMTGVGIA 359
              S+    +  ++        RK    + L+ GA+G I V + H++ +L L    +GI+
Sbjct: 307 CVSSLAAVAWGFLVLSHTSQFKRKFWLRVGLLSGALGFIWVFFTHNQYLLILPFCLIGIS 366

Query: 360 WASILSMPYAMLSGSLPKDKIGIYMGIFNFFIVLPEIIASLGFGWLMRNVLNNDRLLAVQ 419
           + ++ +  +++ + SL     G YMG+FN  I LP+IIAS+   + +  ++       + 
Sbjct: 367 YLTMQTEAFSIFTSSLNGKNEGAYMGLFNCGICLPQIIASVA-SFALFPLIGKSMSGMIL 425

Query: 420 LGGGLMILAAVICYVFIREPKKTDEVLAAK 449
           + G  M+L A        +  + + VL  K
Sbjct: 426 IAGIAMLLGAAAVAAIHEDKPQRNTVLKKK 455


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: 604
Number of extensions: 38
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: 458
Length of database: 459
Length adjustment: 33
Effective length of query: 425
Effective length of database: 426
Effective search space:   181050
Effective search space used:   181050
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