GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Marinicella litoralis KMM 3900

Align Monocarboxylic acid transporter (characterized)
to candidate WP_099018878.1 CCS90_RS07195 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_002591915.1:WP_099018878.1
          Length = 579

 Score =  164 bits (416), Expect = 7e-45
 Identities = 136/499 (27%), Positives = 212/499 (42%), Gaps = 69/499 (13%)

Query: 38  LRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGF 97
           + +      + DFY  G       NG+A A D++SAASF+ + G I+  GYD  +Y +G+
Sbjct: 21  IAIWSKAKNTGDFYVAGKGVHPIANGMATAADWMSAASFISMAGIIAFAGYDASVYLMGW 80

Query: 98  FVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAG 157
              +++  LL+A  LR  G+FT+ + +  R   K  R+ A    + ++  Y+  QM G G
Sbjct: 81  TGGYVLLALLLAPYLRKFGKFTVPEFIGDRYYSKTARIVAVVCLIIISFTYVAGQMRGVG 140

Query: 158 SLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLT 217
            + S  L++       + +GIV      Y +LGGMKG TY Q+ +  +L+    +  V  
Sbjct: 141 IVFSRFLEVEIITGLLIGMGIV----FFYAVLGGMKGITYTQVAQYCVLIFAYMVPAVFI 196

Query: 218 FVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGATLTTQLDFISLALALC 277
            ++ +G     L    E    S +  TK     Q L     Y     + +D   +  AL 
Sbjct: 197 AIQATGNPIPQLAFGSEVVGESVHLLTKLDQIVQDL-GFTAYTEGSKSSIDVFFITAALM 255

Query: 278 LGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLG----YGAAALVGPDRV 333
           +GTAGLPHV++RF+TVP   +ARKS  WA+  I   Y    V+G          + P  V
Sbjct: 256 VGTAGLPHVIVRFFTVPKVSDARKSAFWALFFITILYTTAPVVGALGRMNLIETIQPGEV 315

Query: 334 IAAPGAANAA-----------APLLAFE-------------------------------- 350
             A G    A             LLAFE                                
Sbjct: 316 GTASGNLEYANKPNWFTTWEKTGLLAFEDKNGDGRIQYYNDKNPNFKPTADSYGWQGNEL 375

Query: 351 -LGGSIFMALISAVA----FATVLAVVAGLAITASAAVG----------HDIYNAVIRNG 395
            +   I +     +A    +   L    G+A   S A G          HD+   ++   
Sbjct: 376 TVDRDIMVLANPEIAQLPDWVIALIAAGGIAAALSTAAGLLLVISAAISHDLVKGIMVPN 435

Query: 396 QSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWK 455
            S E +++ V R+      +++  LG       VA +VALAF +AAS+  P IL  ++ K
Sbjct: 436 IS-EKKELMVGRVAAAFAIMVAGYLG-ANPPGFVAQVVALAFGLAASSLFPAILMGIFSK 493

Query: 456 KFNTTGAVAAIYTGLISAL 474
           + N  GA+A +  G++  L
Sbjct: 494 RANKAGAIAGMIVGIVFTL 512


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: 644
Number of extensions: 42
Number of successful extensions: 5
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: 579
Length adjustment: 36
Effective length of query: 515
Effective length of database: 543
Effective search space:   279645
Effective search space used:   279645
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