GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas putida KT2440

Align L-tyrosine transporter (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA

Query= reanno::pseudo5_N2C3_1:AO356_18530
         (471 letters)



>lcl|FitnessBrowser__Putida:PP_1059 PP_1059 Uncharacterized amino
           acid permease YtnA
          Length = 472

 Score =  399 bits (1024), Expect = e-115
 Identities = 201/454 (44%), Positives = 284/454 (62%), Gaps = 12/454 (2%)

Query: 3   GQNSHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMI 62
           GQ +  G LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +I
Sbjct: 10  GQATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVI 69

Query: 63  MRQLGEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWA 122
           MR LGEM V  PVAGSFS +A  Y G  AGFL+GWN W L+++  ++E+TAV  Y+  W 
Sbjct: 70  MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWF 129

Query: 123 PDIPTWVSAAAFFILINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGHG-- 180
           PD+P W+ A A    + A+NL  VK FGE EFWFA+IK+V I+ M+  G  ++  G G  
Sbjct: 130 PDVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGND 189

Query: 181 GPQASVTNLWSHGGFFPNGVSGLVMAMAIIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240
           G    ++NLWS+GGF PNGV+G++M++ ++MF++ G+EM+G TA EA  P+  IP+AI  
Sbjct: 190 GVAVGISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGS 249

Query: 241 VIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSNTAAHILNFV 300
           V +RIL+FY+GAL V+LS+ PW+ +            GSPFV  F  LG  TAA I+NFV
Sbjct: 250 VFWRILLFYVGALFVILSIYPWNEI---------GSQGSPFVMTFERLGIKTAAGIINFV 300

Query: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALSRIDKRGVPVRSILASAAVTLVAVLLN 360
           V+TAALS  N G +   RML  +A+ G AP A +R  K GVP  ++L S    L+ VL N
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLAN 360

Query: 361 YLVPQHALELLMSLVVATLVINWAMISYSHFKFRQHMNQTQQTPLFKALW-YPYGNYICL 419
           YLVP+     + S+     +  W MI  +  KFR  +   ++  L   +W +P  +Y+ L
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLAL 420

Query: 420 AFVVFILGVMLLIPGIQISVYAIPVWVVFMWVCY 453
           AF+V ++G+M      ++++Y  P ++V + V Y
Sbjct: 421 AFLVLVVGLMAYFEDTRVALYIGPAFLVLLTVLY 454


Lambda     K      H
   0.327    0.139    0.432 

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: 659
Number of extensions: 31
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: 471
Length of database: 472
Length adjustment: 33
Effective length of query: 438
Effective length of database: 439
Effective search space:   192282
Effective search space used:   192282
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 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, 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