GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pseudomonas fluorescens FW300-N2C3

Align Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized)
to candidate AO356_17670 AO356_17670 D-alanine/D-serine/glycine permease

Query= TCDB::P24207
         (458 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17670
          Length = 473

 Score =  412 bits (1058), Expect = e-119
 Identities = 198/441 (44%), Positives = 291/441 (65%), Gaps = 3/441 (0%)

Query: 19  LHRGLHNRHIQLIALGGAIGTGLFLGIGPAIQMAGPAVLLGYGVAGIIAFLIMRQLGEMV 78
           L R L  RHI+L+ALG  IG GLFLG   AI+MAGPA++L Y + G+   +IMR LGEM 
Sbjct: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77

Query: 79  VEEPVSGSFAHFAYKYWGPFAGFLSGWNYWVMFVLVGMAELTAAGIYMQYWFPDVPTWIW 138
           V  PV+GSF+ +A  Y GP AGFL+GWNYW ++++  +AE+TA  +YM  WFPDVP WIW
Sbjct: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGIWFPDVPRWIW 137

Query: 139 AAAFFIIINAVNLVNVRLYGETEFWFALIKVLAIIGMI--GFGLWLLFSGHGGEKASIDN 196
           A A  + + ++NL+ V+ +GE EFWFALIK++ II M+  G G+     G+ G    I N
Sbjct: 138 ALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197

Query: 197 LWRYGGFFATGWNGLILSLAVIMFSFGGLELIGITAAEARDPEKSIPKAVNQVVYRILLF 256
           LW +GGF   G +G+++SL ++MF++ G+E+IG+TA EA++P+K+IP A+  V +RILLF
Sbjct: 198 LWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPNAIGSVFWRILLF 257

Query: 257 YIGSLVVLLALYPWVEVKSNSSPFVMIFHNLDSNVVASALNFVILVASLSVYNSGVYSNS 316
           Y+G+L V+L++YPW E+ +  SPFVM F  L     A  +NFV++ A+LS  N G++S  
Sbjct: 258 YVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFSTG 317

Query: 317 RMLFGLSVQGNAPKFLTRVSRRGVPINSLMLSGAITSLVVLINYLLPQKAFGLLMALVVA 376
           RML+ L+  G AP    + S  GVP  +L+LS A   L VL+NYL+P+K F  + ++   
Sbjct: 318 RMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPEKVFVWVTSIATF 377

Query: 377 TLLLNWIMICLAHLRFRAAMRRQGRET-QFKALLYPFGNYLCIAFLGMILLLMCTMDDMR 435
             +  W+MI LA L+FR ++    R   +++  LYP  +YL +AFL +++ LM    D R
Sbjct: 378 GAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVLVVGLMAYFPDTR 437

Query: 436 LSAILLPVWIVFLFMAFKTLR 456
           ++  + P ++V L + F T +
Sbjct: 438 VALYVGPAFLVLLTVLFYTFK 458


Lambda     K      H
   0.329    0.143    0.447 

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: 686
Number of extensions: 35
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: 458
Length of database: 473
Length adjustment: 33
Effective length of query: 425
Effective length of database: 440
Effective search space:   187000
Effective search space used:   187000
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 (21.8 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