GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Pseudomonas putida KT2440

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__Putida:PP_4840
          Length = 468

 Score =  320 bits (820), Expect = 7e-92
 Identities = 171/452 (37%), Positives = 270/452 (59%), Gaps = 7/452 (1%)

Query: 23  EEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALG 82
           E    + + NR +Q+IAIGGAIGTGLF+G+G  + +AGP++  VY+I G   FF++RA+G
Sbjct: 11  EPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 70

Query: 83  ELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDV 142
           EL+L   +  SF+ ++ + LG  A Y  GW Y+  W +TGI D+ A+A Y  +W  F D+
Sbjct: 71  ELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFW--FPDL 128

Query: 143 PQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTG-QPLEGN 201
           PQW+ AL  + ++ ++N++ VK F E+EFWFAL+K++AI+  +  G   + TG     G 
Sbjct: 129 PQWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGFTSPSGR 188

Query: 202 ATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVI 261
                 + ++GG FPHGL+      Q  VFAF  IELVGT A E K+P++ +P+AINS+ 
Sbjct: 189 TAQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSIP 248

Query: 262 WRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSSLNS 321
            RI +FYV +++ ++ + PW     G+SPFV  F   G+P   SI+N VVLT+A SS NS
Sbjct: 249 IRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSANS 308

Query: 322 GLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRV--FE 379
           G++ T R+L  +S  G APK   K+S + VP  G+  +    ++G  L YLVP+ V  F 
Sbjct: 309 GVFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVEAFT 368

Query: 380 IVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSVLVL 439
           +V   +++  +  W  I++  ++ R+       A  ++K+PG  F  ++ L F   +LVL
Sbjct: 369 LVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQAS-NYKMPGGRFMCYVCLSFFAFILVL 427

Query: 440 MAFDYPNGTYTIASLPLIAILLVAGWFGVRRR 471
           ++ +    +  + + P+  ++L   +  VR R
Sbjct: 428 LSLEADTRSALVVT-PIWFVVLAVTYQLVRSR 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: 664
Number of extensions: 34
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: 468
Length adjustment: 34
Effective length of query: 463
Effective length of database: 434
Effective search space:   200942
Effective search space used:   200942
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