GapMind for catabolism of small carbon sources

 

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

Align L-alanine and D-alanine permease (characterized)
to candidate WP_033100257.1 JG50_RS0106285 amino acid permease

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>NCBI__GCF_000763315.1:WP_033100257.1
          Length = 446

 Score =  305 bits (780), Expect = 3e-87
 Identities = 164/436 (37%), Positives = 251/436 (57%), Gaps = 9/436 (2%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           L+++L  RH+++MALG  IG G+F GSA+ I  AGP ++ SY + G+ + ++M A+ EMA
Sbjct: 5   LQKQLLPRHVQMMALGGAIGAGIFQGSAETISAAGPGVIFSYALAGILLYIVMSAMAEMA 64

Query: 78  VHNPVAGSFSR-YAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWI 136
           +    AG+  R       G    F+ GW Y+  W++    EI     ++  WF  VP W+
Sbjct: 65  LG--FAGTDLRGLVHKAFGTRVSFILGWLYFIQWVLVMAVEIVTAGTFLQYWF-SVPVWL 121

Query: 137 WALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGIS 196
            +L   + + +INL +V+ FGE E+W   +KIVT+I  VI G  ++ FG      A G++
Sbjct: 122 LSLIVTLVIIAINLFSVRLFGEIEYWLTSVKIVTLIVFVILGA-LLLFGIIPSAQAPGLT 180

Query: 197 NLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILL 256
           N   HGGF P G  GVL SL +V+F+Y G EMIGLT  E K+ +KT+P  I  V  RI L
Sbjct: 181 NYRVHGGFFPLGWQGVLSSLLIVIFSYGGTEMIGLTITEMKDAKKTLPRVIKGVILRICL 240

Query: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316
           FYV  L +I  + PW+++ + GSPFV     +G+K  A I+NF+++TA +S+ N G+++T
Sbjct: 241 FYVLPLLIITGLIPWDQVKSSGSPFVEVLSAVGLKGVANIMNFILLTAVISAANSGMYAT 300

Query: 317 GRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIAT 376
            RMLYSLA   +APA F +    GVP  AL  S   L LG L+ ++ PE VF ++  I  
Sbjct: 301 TRMLYSLAGEKEAPAFFTRLGKRGVPIYALAASSVCLFLGSLVAFIAPESVFQYLMGIPG 360

Query: 377 FGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDT 436
           +  I TW++I L+ LK R     +      +R+  +P ++ + L  L  ++  +   P  
Sbjct: 361 YTVILTWILICLSHLKLRGKYERTP----DFRLSFFPFTTGITLIVLAAIMIFVLLSPKN 416

Query: 437 RVALYVGPAFLVLLTV 452
            +   V  A +++LT+
Sbjct: 417 LINTIVYLAIILVLTI 432


Lambda     K      H
   0.328    0.142    0.444 

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: 504
Number of extensions: 25
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: 473
Length of database: 446
Length adjustment: 33
Effective length of query: 440
Effective length of database: 413
Effective search space:   181720
Effective search space used:   181720
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 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