GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas putida KT2440

Align L-alanine and D-alanine permease (characterized)
to candidate PP_4495 PP_4495 aromatic amino acid transport protein

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>FitnessBrowser__Putida:PP_4495
          Length = 472

 Score =  409 bits (1052), Expect = e-119
 Identities = 207/454 (45%), Positives = 292/454 (64%), Gaps = 12/454 (2%)

Query: 10  GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVI 69
           G+    G LKR L  RHI+L+ALG  IG GLFLGSA  ++ AGP+++L Y I G    +I
Sbjct: 3   GQNMHSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVMKSAGPSMILGYAICGFIAFMI 62

Query: 70  MRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWF 129
           MR LGEM V  PVAGSFS +A  Y G  AGFL+GWN W L+++  ++E++AV  Y+  W+
Sbjct: 63  MRQLGEMIVEEPVAGSFSHFAHTYWGGFAGFLSGWNCWVLYILVGMSELSAVGKYVHYWW 122

Query: 130 PDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGND 189
           P++P W+ A A  V + +INL+ VK FGE EFWFA+IK+V I++M+  G+G      G+ 
Sbjct: 123 PEIPTWVTAAAFFVLINAINLMNVKFFGEAEFWFAIIKVVAIVSMI--GLGAYLLTSGSG 180

Query: 190 GVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGS 249
           G    ++NLW HGGF PNGVSG++M+L  +MF++ G+EM+G TA EA  P+  IP AI  
Sbjct: 181 GPEATVANLWTHGGFFPNGVSGLVMALAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240

Query: 250 VFWRILLFYVGALFVILSIYPWNEI--------GTQG-SPFVMTFERLGIKTAAGIINFV 300
           V +RIL+FYVGAL V+LS+ PW+ +        G+ G SPFV  F  LG   AA ++NFV
Sbjct: 241 VIYRILIFYVGALVVLLSLTPWDNLVASIDASGGSYGSSPFVQVFSLLGSDVAANLLNFV 300

Query: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLN 360
           V+TAALS  N G +   RML  +A+ G APA  AK    GVP R++L+S A   + VLLN
Sbjct: 301 VLTAALSVYNSGTYCNARMLLGMAEQGDAPASLAKVDKRGVPVRSILVSAAVTFVAVLLN 360

Query: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420
           YL+P+     + S+     +  W MI  + LKFR+ L  + +  L   +W YP  +Y+ L
Sbjct: 361 YLMPQNALELLMSLVVATLVINWAMISYSHLKFRQHLDRTGQKPLFKALW-YPYGNYVVL 419

Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLF 454
           AF+VL++G+M   P  +V++Y  P +L+ + V++
Sbjct: 420 AFVVLILGIMLMIPGIQVSVYAIPVWLLAMLVVY 453


Lambda     K      H
   0.328    0.142    0.444 

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: 630
Number of extensions: 29
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: 473
Length of database: 472
Length adjustment: 33
Effective length of query: 440
Effective length of database: 439
Effective search space:   193160
Effective search space used:   193160
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 (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