GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ansP in Pseudomonas fluorescens FW300-N1B4

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate Pf1N1B4_3559 Aromatic amino acid transport protein AroP

Query= TCDB::P40812
         (497 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3559 Aromatic amino acid
           transport protein AroP
          Length = 473

 Score =  322 bits (826), Expect = 1e-92
 Identities = 171/462 (37%), Positives = 277/462 (59%), Gaps = 18/462 (3%)

Query: 20  NAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILR 79
           N+H     + + NR +Q+IA+GGAIGTGLFLG+   L+ AGP++ L Y ICG  +F I+R
Sbjct: 5   NSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMR 64

Query: 80  ALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAF 139
            LGE+++  P +GSF  +A ++ G  A +++GW  +I + + G+ ++TAV  Y+HYW   
Sbjct: 65  QLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP- 123

Query: 140 GDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPLE 199
            D+P WV A G   ++  +N+  VK F E EFWFA+IKV+AIV  + +G+  L +G    
Sbjct: 124 -DIPTWVSAAGFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGD--G 180

Query: 200 GNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINS 259
           G       + ++GGFFP+G+   ++ +  ++F+F  +E++G  A E   P+ ++PKAIN 
Sbjct: 181 GPQASVTNLWEHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240

Query: 260 VIWRIGLFYVGSVVLLVLLLPWNAYQA---------GQSPFVTFFSKLGVPYIGSIMNIV 310
           VI+RI +FY+G++V+L+ L PW++              SPFV  FS LG      I+N V
Sbjct: 241 VIYRILIFYIGALVVLLSLTPWDSLLTTLNASGDAYSGSPFVQVFSMLGSDTAAHILNFV 300

Query: 311 VLTAALSSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLN 370
           VLTAALS  NSG YC  R+L  M+  G APK ++K+ ++ VP   ILA+  V +V V LN
Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSKIDKRGVPVRSILASAAVTLVAVLLN 360

Query: 371 YLVPSRVFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTL 430
           YLVP    E++++     ++ +WA I     + RQ + + K   + FK    P+ +++ L
Sbjct: 361 YLVPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNKTKQTPL-FKALWYPYGNYVCL 419

Query: 431 LFLLSVLVLMAFDYPNGTYTIASLPL-IAILLVAGWFGVRRR 471
            F++ +L +M    P    ++ ++P+ +A + V   +G++ +
Sbjct: 420 AFVVFILGVMLL-IPGIQISVYAIPVWVAFMWVC--YGIKNK 458


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: 633
Number of extensions: 33
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: 497
Length of database: 473
Length adjustment: 34
Effective length of query: 463
Effective length of database: 439
Effective search space:   203257
Effective search space used:   203257
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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