GapMind for catabolism of small carbon sources

 

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

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_033101984.1 JG50_RS0115245 amino acid permease

Query= TCDB::P40812
         (497 letters)



>NCBI__GCF_000763315.1:WP_033101984.1
          Length = 484

 Score =  265 bits (677), Expect = 3e-75
 Identities = 162/456 (35%), Positives = 251/456 (55%), Gaps = 27/456 (5%)

Query: 33  RQVQMIAIGGAIGTGLFLGAGARLQMAGPALALV-YLICGIFSFFILRALGELVLHRPSS 91
           R + MIAIGG+IGTG+FL +GA +  AGP  ALV YL  GI  +F++ +LGE+    P +
Sbjct: 17  RHLSMIAIGGSIGTGVFLASGASISEAGPGGALVAYLAIGIMVYFLMTSLGEMATFMPVA 76

Query: 92  GSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVFALGA 151
           GSF +YA  F+     +  GW Y+ NWA+T  V+++A +L M YW  F   P  +++   
Sbjct: 77  GSFSTYAGRFVDPALGFAMGWNYWYNWAITIAVELSAGSLIMDYW--FPHSPSILWSALF 134

Query: 152 LTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLEGNATGFHLITDN 211
           L ++  +N + VK + E E+WF+ IKV  ++IF+V+G + +     + G A GF   T N
Sbjct: 135 LLLMFGLNALSVKGYGESEYWFSFIKVATVIIFIVIGLLMIFG--IMGGEAIGFKNFTIN 192

Query: 212 GGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIGLFYVGS 271
              F HG L  L +     F+F   ELVG AAGE ++P+K VPKAI  V WRI LFY  +
Sbjct: 193 DAPFHHGWLGILSVFMIAGFSFQGTELVGVAAGESENPRKNVPKAIRQVFWRILLFYALA 252

Query: 272 VVLLVLLLPW--------NAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNSGL 323
           ++++ L+LP+        +  Q  +SPF   F K G+ +  S+MN V+LT+ LS+ NSG+
Sbjct: 253 ILVMGLVLPYTNPNLVGGDVNQIAKSPFTIIFEKAGLAFAASVMNAVILTSVLSAGNSGM 312

Query: 324 YCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVFEIVLN 383
           Y + R+L  M+  G APK  AK++R+ VP   +L T  V  V    + +   +++  +LN
Sbjct: 313 YASTRMLWQMAKEGKAPKLFAKVNRRGVPVFALLLTTAVGAVAFLASLVGQGKIYIWLLN 372

Query: 384 FASLGIIASWAFIMVCQMRLRQA-IKEGKAAD-VSFKLPGAPFTSWLTLLFLLSVLV--- 438
            + L    +W  I +   R R+A + +G+  + + ++    PF     L+  + V+V   
Sbjct: 373 ASGLSGFIAWLGIAISHYRFRRAYVAQGRDLNHLVYRAKWFPFGPLFALVLCVIVIVGQN 432

Query: 439 LMAF-----DYPNGTYTIASLPLIAILLVAGWFGVR 469
             AF     D+     +   LPL  +L    W G +
Sbjct: 433 YQAFTGNTIDWNGILVSYIGLPLFILL----WLGYK 464


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: 734
Number of extensions: 58
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: 497
Length of database: 484
Length adjustment: 34
Effective length of query: 463
Effective length of database: 450
Effective search space:   208350
Effective search space used:   208350
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: 52 (24.6 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