GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ansP in Dyella japonica UNC79MFTsu3.2

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= TCDB::P40812
         (497 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3653 N515DRAFT_3653 amino
           acid/polyamine/organocation transporter, APC superfamily
           (TC 2.A.3)
          Length = 453

 Score =  330 bits (846), Expect = 6e-95
 Identities = 168/435 (38%), Positives = 260/435 (59%), Gaps = 20/435 (4%)

Query: 33  RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLHRPSSG 92
           R +  +A+G AIG GLFLG+   + +AGP++   YL  G   F I+RALGE+ +H P +G
Sbjct: 12  RHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMAVHDPVAG 71

Query: 93  SFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFALGAL 152
           SF +YA  +LG  A Y+ GW Y+I     G+ + TAV +YM  W  F ++PQW++  G++
Sbjct: 72  SFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQW--FPELPQWIWVFGSV 129

Query: 153 TIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV--VGTIFLGTGQPLEGNATGFHLITD 210
            ++G +N++ VK + EMEFWF LIKV+ +V+ ++   G I+LG G    G   G   +  
Sbjct: 130 AMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGN--GGQPVGLANLWS 187

Query: 211 NGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYVG 270
           +GG+FPHG    ++ +  VVFAF  IE +G AAGE   P++ +P+A+NSV+WRI +FYVG
Sbjct: 188 HGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIFYVG 247

Query: 271 SVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGLYCTGRIL 330
           ++ +++ + PW+      SPFVT F KLG+P    ++N VV+TAALS  NS  +   R+L
Sbjct: 248 ALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGSRML 307

Query: 331 RSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLNFASLGII 390
            S+S    AP F+ ++S   VP   +L TL   V GV LNYL+P R+F ++++  +   +
Sbjct: 308 YSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERIFAMMMSILAFNTV 367

Query: 391 ASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVLMAFDYPNGTYT 450
            +W  +++     R+  + G  A   F L   P TS + LLFL  VL ++ +        
Sbjct: 368 WTWMMVLIAHYSFRR--RHGATA---FPLRAWPLTSVVCLLFLAFVLFMLGY-------- 414

Query: 451 IASLPLIAILLVAGW 465
            ++   +A+ + AGW
Sbjct: 415 -SADTRVALYVGAGW 428


Lambda     K      H
   0.328    0.140    0.434 

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: 666
Number of extensions: 33
Number of successful extensions: 2
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: 497
Length of database: 453
Length adjustment: 33
Effective length of query: 464
Effective length of database: 420
Effective search space:   194880
Effective search space used:   194880
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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