GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Thermoactinomyces daqus H-18

Align The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized)
to candidate WP_160173842.1 JG50_RS0109790 amino acid permease

Query= TCDB::K7VV21
         (488 letters)



>NCBI__GCF_000763315.1:WP_160173842.1
          Length = 453

 Score =  262 bits (670), Expect = 2e-74
 Identities = 141/390 (36%), Positives = 225/390 (57%), Gaps = 17/390 (4%)

Query: 13  VKRGLKSRHVSMIALGGTIGTGLFLTSGDVIHTAGPFGALTAYVLIGAMVYFLMTSLGEM 72
           ++R L  R + MI LG  IGTGLF+ S   IH AGP G L +Y+L   +V  ++  L  +
Sbjct: 15  LQRSLSERQMIMIGLGSAIGTGLFMGSSLTIHYAGP-GVLFSYLLSSLIVLAMVFCLSRL 73

Query: 73  ATYLPTSGSFSDYGTRYVDPAFGFALGWNYWLNWAITVAVDLTAVALCIKFWLPDVPSWI 132
           +   PT+GSF  +   Y+   FGFA+ + YW   AI +  + TA+ L +K+W P +PSWI
Sbjct: 74  SVIHPTAGSFGLHAETYLGSWFGFAVRFTYWAANAIVIGGEATAIGLYMKYWFPGLPSWI 133

Query: 133 FSLIALIIVFSINALSVKTFGETEYWLSAIKITVVVLFLIIGFLSIFGIMGGHIDVAKNL 192
           + +   +++  INA+SV++FG  EYW S +K+  V+ F+++G   IFG          N 
Sbjct: 134 WIIAFSLLIIGINAISVQSFGWFEYWFSTLKVVAVIGFILLGIALIFG----------NS 183

Query: 193 SVGNHGFVGGLGSFTTGG--GILGVLLVAGFSFQGTELLGITAGEAENPEKSIPKAMNSI 250
           +   H ++   G F   G  G+     +A FSF GTE++ ITAGEA+ P++++ +AM  +
Sbjct: 184 TQSTH-YLLAYGGFLPHGWKGVWMGSAMAMFSFMGTEIIAITAGEAKKPKQALTRAMKWM 242

Query: 251 FWRILVFYILSIFVMAAIIPFTDPHLVGGNSAAQSPFTIVFERVGFSIAASIMNAVVLTS 310
             R+++FY+LS  VM  I+P+     +GG    +SPF  V + +    AA +MN ++LT+
Sbjct: 243 VARLVIFYLLSTLVMVCIVPWNQ---IGGEQIQESPFVKVLQSLHIPYAAGVMNFIILTA 299

Query: 311 VVSAANSGMYASTRMLYSLAKDGGAPTIFSKTSKNGIPFIALLATTAVALLTFLTSIYGV 370
            +S  N+ +YA TRM++SL+K G AP +F K ++ GIP +AL+ ++    +  L +++  
Sbjct: 300 ALSTMNANLYACTRMMFSLSKSGYAPAVFGKVNRRGIPLMALIVSSFGLGVAVLLNMFDP 359

Query: 371 SFFTFLVSASGLTGFIAWIGIAISHFRFRR 400
             +  L   S   G   WI I +S+ R RR
Sbjct: 360 QAYNTLFGISIFGGIFTWITIFLSYARLRR 389


Lambda     K      H
   0.326    0.141    0.425 

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: 585
Number of extensions: 30
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: 488
Length of database: 453
Length adjustment: 33
Effective length of query: 455
Effective length of database: 420
Effective search space:   191100
Effective search space used:   191100
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 (21.6 bits)
S2: 51 (24.3 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