GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Rhodobacter ovatus JA234

Align Monocarboxylic acid transporter (characterized)
to candidate WP_097031687.1 CRO07_RS16135 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_900207575.1:WP_097031687.1
          Length = 554

 Score =  395 bits (1014), Expect = e-114
 Identities = 224/540 (41%), Positives = 327/540 (60%), Gaps = 30/540 (5%)

Query: 20  ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGI 79
           ++ I++F+ F+  T+ +     + T  ++DFYT G   +G QNGLAIAGDY+SAA+FLG+
Sbjct: 37  VIAIAMFLFFVAATLGLTAWAARRTKSASDFYTAGGGITGFQNGLAIAGDYMSAAAFLGV 96

Query: 80  VGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAAC 139
            G +   G DG  Y++G+ V W + L ++AE LRN+GRFT ADV SFRL Q  +R  +A 
Sbjct: 97  SGMVFGKGVDGVFYTVGWTVGWPLILFMIAERLRNLGRFTFADVASFRLEQTRIRTLSAF 156

Query: 140 GTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQ 199
           G L V +FYLIAQM GAG L+ +L  +      A  V +VG++M+ YV  GGM  TT+VQ
Sbjct: 157 GALTVVIFYLIAQMVGAGKLIQLLFGLE----YAYAVILVGVLMMLYVTFGGMLATTWVQ 212

Query: 200 MIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQY 259
           + KAVLL+ G  ++ +L           ++  A++ HAA +           IL P    
Sbjct: 213 ITKAVLLLSGCTLLVLLGLKHFGFSPEAMMQAAIDNHAAHE----------AILSP---- 258

Query: 260 GATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLV 319
            ++++  +  ISLALAL  G AGLPH+LMRF+TVP AKEARKSV +A   IG F+++ + 
Sbjct: 259 SSSISDPITAISLALALMCGPAGLPHILMRFFTVPDAKEARKSVFYATGFIGYFFMLAVT 318

Query: 320 LGYGAAALVGP-----DRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374
           +G+ A  LVG      D      G  N AA  L+ E+GG +F+  ISAVAFAT+LAVV+G
Sbjct: 319 IGFLAITLVGTNPAYLDEAGKLLGGGNMAAIHLSGEVGGDVFLGFISAVAFATILAVVSG 378

Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434
           LA++ ++AV HD+Y  VI+ G++++  ++ VSR+  +V+G+++I LG++   QN+AF+V+
Sbjct: 379 LALSGASAVSHDLYARVIKKGRASDKTEMMVSRMATLVLGVLAIALGLVFENQNIAFMVS 438

Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494
           LAF +AAS N P +  S++WK   T GA      GL SA+  + L P V  N    V G 
Sbjct: 439 LAFGLAASVNFPVLFLSIFWKNMTTRGAFIGGLMGLFSAVGCVVLGPTVWVN----VLGF 494

Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPD--NMDDLAAEME-VRSLTGVGVEKAVDH 551
           + AIFP +   L S+  AF   W  ++  + +   +D      + VRS TG+G   AV H
Sbjct: 495 ETAIFPWEQYALFSMTAAFGGIWFFSVTDRSERAKLDKAGFPAQFVRSETGLGAAGAVAH 554


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: 673
Number of extensions: 31
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: 551
Length of database: 554
Length adjustment: 36
Effective length of query: 515
Effective length of database: 518
Effective search space:   266770
Effective search space used:   266770
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