GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Azospirillum brasilense Sp245

Align Monocarboxylic acid transporter (characterized)
to candidate AZOBR_RS19235 AZOBR_RS19235 actetate permease

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__azobra:AZOBR_RS19235
          Length = 556

 Score =  416 bits (1069), Expect = e-120
 Identities = 236/540 (43%), Positives = 329/540 (60%), Gaps = 36/540 (6%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I++F++F+  T+ +     K T  ++DFYT G   SG QNGLAIAGDY+SAA+FLG+ G 
Sbjct: 42  IAMFLLFVAGTLGITYWASKRTRSASDFYTAGGGISGFQNGLAIAGDYMSAAAFLGLSGM 101

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +   G+DG +Y+IGF V W + L L+AE LRN+GRFT ADV S+RL Q P+R  AA G+L
Sbjct: 102 VFAKGFDGVIYTIGFLVGWPLMLFLIAERLRNLGRFTFADVASYRLGQTPIRSLAAVGSL 161

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V  FYLIAQM GAG L+ +L  +         V +VG++MI YV  GGM  TT+VQ+IK
Sbjct: 162 TVVCFYLIAQMVGAGKLIQLLFGLD----YTYAVVMVGVLMILYVTFGGMLATTWVQIIK 217

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           AV+L+GG  ++  L   +       LL  AV  HAA+            IL P     A 
Sbjct: 218 AVMLLGGCTVLVGLALAQFGFNPERLLQQAVAAHAAN----------AAILRP----SAA 263

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
           +   +  +SL+LAL  G AGLPH+LMRF+TVP AKEARKSV +A   IG F+++T+ +G+
Sbjct: 264 MADPIAAVSLSLALMCGPAGLPHILMRFFTVPDAKEARKSVVYATGFIGYFFILTVTIGF 323

Query: 323 GAAALVG--PDRVIAAP---GAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377
            A  +VG  P  + AA    G  N AA  L+  +GG++F+  ISAVAFAT+LAVVAGL +
Sbjct: 324 LAIVIVGTNPAYLDAAGKILGGGNMAAIHLSKAIGGNLFLGFISAVAFATILAVVAGLTL 383

Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437
             ++AV HD+Y  V++ G +TEA ++RVSR+  + +G+I+I LG+L   QN+AF+V LAF
Sbjct: 384 AGASAVSHDLYARVLKKGNATEASEMRVSRLATLALGVIAITLGLLFENQNIAFMVGLAF 443

Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWA 497
            +AAS N P ++ S++WK   T GA    + GL+S +  + L P V       V      
Sbjct: 444 GLAASVNFPVLILSIFWKGLTTRGAFIGGFAGLVSCVAFVVLGPTV----WVSVFKFPAP 499

Query: 498 IFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME------VRSLTGVGVEKAVDH 551
           IFP ++P L S+ +AF   W+ ++    D     AAE +      +RS TG+G   A  H
Sbjct: 500 IFPYEHPALFSMVIAFATTWLFSVT---DRSARAAAEAKAYEYQYIRSETGLGAASAASH 556


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: 690
Number of extensions: 35
Number of successful extensions: 5
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: 556
Length adjustment: 36
Effective length of query: 515
Effective length of database: 520
Effective search space:   267800
Effective search space used:   267800
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 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