GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cit1 in Sulfuricurvum kujiense DSM 16994

Align The pmf-dependent citrate uptake system, Cit1 (characterized)
to candidate WP_013459243.1 SULKU_RS01940 DASS family sodium-coupled anion symporter

Query= TCDB::Q6D017
         (484 letters)



>NCBI__GCF_000183725.1:WP_013459243.1
          Length = 467

 Score =  297 bits (761), Expect = 5e-85
 Identities = 165/470 (35%), Positives = 258/470 (54%), Gaps = 16/470 (3%)

Query: 14  MIVILVIAAFFWQMEPPAGLNPAAWHSAVIFVATIVCIVANVLPIGAIGIISITLFALTY 73
           ++++ + A   W   PP  ++P AW    IF+ TI+ I+ NVLPI A  +I++ +  L  
Sbjct: 11  VVLLGMFALTLWLTPPPLAISPKAWQLFTIFLTTIIAILGNVLPIIAASVIALAISVLF- 69

Query: 74  AAGDKTASGAIQT--ALSDLNSSLIWLIVVAFMIARGFIKTGLGRRIALQMIRLLGKRTL 131
                   G I+   A +  + S I +I+ AF+++    K+GLG+R++L +IR  G  TL
Sbjct: 70  --------GVIEPVKAYAGFSESFILMIIAAFLVSHAVHKSGLGKRLSLHIIRRFGHSTL 121

Query: 132 GLAYGLAFADLVLSPAMPSNTARCGGIIYPIADSLSRSFDSKPEDASRSKIGTFLITCIG 191
           GL Y L   D++++PA PSNTAR  G++YPI   L+    SK  D ++ + G++L+    
Sbjct: 122 GLGYSLIATDILIAPAFPSNTAR-SGVLYPIVYGLAHDCGSKVGDNTQRRAGSYLMMTSM 180

Query: 192 NVNDVTAAMFMTAYTGNLLAVKLAANAGVTITWGSWFLAALVPCLISLAIVPLLVYWLTK 251
               +++ +++TA   N + V +A   G+ IT+GSW L A+VP LI+ A++P ++Y +  
Sbjct: 181 AGLTISSGLWLTAMAVNPVGVGIAETMGIHITFGSWLLYAIVPTLIAFALIPWMLYRIYP 240

Query: 252 PEIRHTPDAPKLAVAELAKMGSISRGEWLMAFTVILLLVLWIFGDRLGVDATTASFVGLS 311
           PE+R TPDAP+ A   L  MG ISR EW+ A   I +L  W     LG+D    +F GL 
Sbjct: 241 PELRSTPDAPQKAKEALEHMGRISRNEWITAGVFISMLTFWALSGVLGIDKAAVAFGGLG 300

Query: 312 FLLLTGVLSWEDVKNEKGAWDTLIWFAALLMMANQLKKLGFTNWFGDLIGSNIGHLMQGT 371
            L+ T V   ED +++  A  TLIWFA L  ++ QL ++GF       + S+    + G 
Sbjct: 301 ILMATRVFGVEDFRSQGEALSTLIWFAILFALSTQLAEMGFMG----AVASHFTLYLVGL 356

Query: 372 SWVLVLLLLNAAYFYTHYFFASGNAQIAALFAVFLGVGINLNIPAVPMAFMLAFTSSLYC 431
           SW+ V +LL A Y   HY F S +A + ALF +FL VG+   +P   MA ML F ++   
Sbjct: 357 SWMWVYILLIAVYVLIHYLFVSQSAHLLALFGIFLAVGVGAGVPGELMAMMLLFATNFNA 416

Query: 432 SLTQYTHARGPILFGAGYVPTAVWWRTGFVVSLVNQAIFMGAGLLWWKAI 481
           ++T    +   I   +GY+     +  G  V+L+   +FM  G  W  A+
Sbjct: 417 TITPQGSSCNAIYLSSGYISAREIYIYGGAVTLLTFLVFMIIGTPWILAL 466


Lambda     K      H
   0.327    0.139    0.440 

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: 739
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: 484
Length of database: 467
Length adjustment: 33
Effective length of query: 451
Effective length of database: 434
Effective search space:   195734
Effective search space used:   195734
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 Apr 09 2024. 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