GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Pseudomonas fluorescens FW300-N2E2

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= TCDB::P15993
         (457 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  396 bits (1018), Expect = e-115
 Identities = 195/444 (43%), Positives = 281/444 (63%), Gaps = 4/444 (0%)

Query: 8   GEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFLIMRQLG 67
           G  LKR L  RHI+L+ALG  IG GLFLGSA  I+ AGP I+L Y I G    +IMR LG
Sbjct: 15  GGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALG 74

Query: 68  EMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFWYPEIPT 127
           EM V  PVAGSFS +A  Y G  AGF +GWNYW L+++  +AE+TAV  Y+  W+P++P 
Sbjct: 75  EMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPR 134

Query: 128 WVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFG-GWLLFS-GNGGPQAT 185
           W+ A    V + +INL  VK FGE EFWFA+IK++ ++AM+I G G + F  GN G    
Sbjct: 135 WIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALG 194

Query: 186 VSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRI 245
           +SNLW  GGF+P+G  G++M + ++MF++ G+E++G+TA EA NP+++IP A   V +RI
Sbjct: 195 ISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRI 254

Query: 246 LIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVY 305
           L+FY+G+L V+LS+ PW  +    SPFV+ F  LG    A  +N VV+TAALS  N  ++
Sbjct: 255 LLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIF 314

Query: 306 CNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPESAFGLLMAL 365
              RML+ LAQ G AP   A+    GVP   +L+S     L VL+NYL PE  F  + ++
Sbjct: 315 STGRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSI 374

Query: 366 VVSALVINWAMISLAHMKFRRA-KQEQGVVTRFPALLYPLGNWICLLFMAAVLVIMLMTP 424
                +  W MI LA +KFR++    +    ++   LYP+ +++ L F+  V+ +M   P
Sbjct: 375 ATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFP 434

Query: 425 GMAISVYLIPVWLIVLGI-GYLFK 447
              +++Y+ P +L++L +  Y+FK
Sbjct: 435 DTRVALYVGPAFLVLLTVLFYVFK 458


Lambda     K      H
   0.328    0.141    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: 695
Number of extensions: 28
Number of successful extensions: 2
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: 457
Length of database: 473
Length adjustment: 33
Effective length of query: 424
Effective length of database: 440
Effective search space:   186560
Effective search space used:   186560
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 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