GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Paraburkholderia bryophila 376MFSha3.1

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate H281DRAFT_04042 H281DRAFT_04042 aromatic amino acid:proton symporter, AAT family

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__Burk376:H281DRAFT_04042
          Length = 506

 Score =  333 bits (853), Expect = 1e-95
 Identities = 171/467 (36%), Positives = 280/467 (59%), Gaps = 7/467 (1%)

Query: 8   AAEQHAAKRRWLNA-HEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALV 66
           A E H   R   NA  ++G  + + NR +Q+IA+GGAIGTGLFLG+ + LQ AGP++ L 
Sbjct: 36  AIEIHTLGRNLDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILG 95

Query: 67  YLICGIFSFFILRALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDI 126
           Y I G+ +F I+R LGE+V   P +GSF  +A ++ G+   +++GW Y++ + +  + ++
Sbjct: 96  YAIGGVIAFMIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAEL 155

Query: 127 TAVALYMHYWGAFGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLV 186
           TAV  Y+HYW  +  VP WV AL     +  +N+  VK + E EFWFA+IKV+A++  ++
Sbjct: 156 TAVGTYVHYW--WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMIL 213

Query: 187 VGTIFLGTGQPLEGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGEC 246
            G   L +G    G       +  +GGFFPHG      ++  ++F+F  +EL+G  A E 
Sbjct: 214 FGGYLLVSGHG--GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEA 271

Query: 247 KDPQKMVPKAINSVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSI 306
            +PQK +PKA+N VI+RI +FY+ S+ +L+ L PWN   AG SPFV  FS++G     ++
Sbjct: 272 DEPQKSIPKAVNQVIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANV 331

Query: 307 MNIVVLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVG 366
           +N+VVLTAALS  NSG+Y   R+L  ++  G+AP+ + K+ R+ VPY  I  + +     
Sbjct: 332 LNVVVLTAALSVYNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTC 391

Query: 367 VFLNYLVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTS 426
           V +NYL+P+    +++      ++ +WA I +  ++ R+A+       + FK    P ++
Sbjct: 392 VIVNYLIPAEALGLLMALVVAALVLNWALISLTHLKSRRAM-VAAGETLVFKSFWFPVSN 450

Query: 427 WLTLLFLLSVLVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVA 473
           W+ L F+  +LV++A   P  + ++  +P+  +++ AG+   RRR A
Sbjct: 451 WICLAFMALILVILAMT-PGLSVSVLLVPVWLVVMWAGYAFKRRRAA 496


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: 689
Number of extensions: 37
Number of successful extensions: 3
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: 506
Length adjustment: 34
Effective length of query: 463
Effective length of database: 472
Effective search space:   218536
Effective search space used:   218536
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 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:

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