GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Marinobacter algicola DG893

Align Monocarboxylic acid transporter (characterized)
to candidate WP_007154786.1 MDG893_RS15635 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_000170835.1:WP_007154786.1
          Length = 588

 Score =  147 bits (371), Expect = 1e-39
 Identities = 89/279 (31%), Positives = 142/279 (50%), Gaps = 7/279 (2%)

Query: 38  LRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGF 97
           + +      ++DFY  G       NG AI  D++SAASF+ + G I+  GY    + +G+
Sbjct: 21  IAIWAKAGSTSDFYVAGGGVHPITNGAAIGADWMSAASFISMAGLIAAGGYANSTFLMGW 80

Query: 98  FVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAG 157
              +++  +L+A  LR  G+FT+ + +  R   K  R+ A    +  ++ Y+I QMAGAG
Sbjct: 81  TGGYVLLAMLLAPYLRKFGKFTVPEFIGDRFYSKNARLVAVICLIVASVTYVIGQMAGAG 140

Query: 158 SLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLT 217
              S  L++       + + I  IV+  Y +LGGMKG TY Q+ +  +L+    I  V  
Sbjct: 141 VAFSRFLEVD----ATMGLIIAAIVVFVYAVLGGMKGITYTQVAQYCVLITAYTIPAVFI 196

Query: 218 FVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGL-QYGATLTTQLDFISLALAL 276
            ++++G     L      H  S        +   I + G  +Y A +  +L+ +   L L
Sbjct: 197 SLQLTGNALPPLG-LFSTHVDSGMPILDKLNQV-ITDLGFNEYTADVDNKLNMVLFTLTL 254

Query: 277 CLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYL 315
            +GTAGLPHV++RF+TVP   +AR S  WA+V I   YL
Sbjct: 255 MIGTAGLPHVIIRFFTVPKVADARWSAGWALVFIALLYL 293



 Score = 67.4 bits (163), Expect = 1e-15
 Identities = 42/123 (34%), Positives = 68/123 (55%), Gaps = 2/123 (1%)

Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416
           + LI+A   A  L+  AGL +  S+AV HD+    I N   TE  ++  +RI++ V  ++
Sbjct: 394 IGLIAAGGLAAALSTAAGLLLAISSAVSHDLIKGSI-NPNITEKGELMAARISMAVAIVV 452

Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476
           +  LG        A +VALAF +AA++  P ++  ++ K+ N  GA+A + TGL   L  
Sbjct: 453 ATYLGANP-PGFAAQVVALAFGIAAASLFPALMMGIFSKRVNNVGAIAGMLTGLAFTLSY 511

Query: 477 IFL 479
           IF+
Sbjct: 512 IFV 514


Lambda     K      H
   0.324    0.138    0.393 

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: 635
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 588
Length adjustment: 36
Effective length of query: 515
Effective length of database: 552
Effective search space:   284280
Effective search space used:   284280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 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