GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ppa in Burkholderia phytofirmans PsJN

Align Phenylacetate permease, Ppa (characterized)
to candidate BPHYT_RS11800 BPHYT_RS11800 acetate permease

Query= TCDB::O50471
         (520 letters)



>FitnessBrowser__BFirm:BPHYT_RS11800
          Length = 528

 Score =  397 bits (1021), Expect = e-115
 Identities = 215/527 (40%), Positives = 325/527 (61%), Gaps = 22/527 (4%)

Query: 6   ISMFMVFVCFTLLVTRWAALRTRSASDFYTAGGGLTGMQNGLAIAGDMISAASFLGISAM 65
           I  F+ F+  +L++T W+A R+R  S F+ AG  L+  QNGLA+AGD +SA SFLG++ +
Sbjct: 12  IIAFVGFIGLSLVLTGWSARRSRGTSGFFVAGRNLSPFQNGLALAGDFMSAGSFLGVTGL 71

Query: 66  MFMNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLAQTPVRLTSAFGTL 125
           + + G+DG++Y +G +AGW +I+ ++AE +RN GKYT +DVV+ RL    VR  ++  +L
Sbjct: 72  VSLFGFDGIVYQVGFIAGWIMIMLIVAEPVRNCGKYTLSDVVALRLRSRGVRAATSVSSL 131

Query: 126 VVALMYLVAQMVGAGKLIELLFGISYLYAVMLVGVLMVAYVTFGGMLATTWVQIIKAVML 185
           + +L YL+AQ+VG G L  LL  I    A++L+G+LM+AYV FGGM+A T+VQI+KAV++
Sbjct: 132 ITSLAYLLAQLVGGGALASLLLPIGTNAAIVLIGILMIAYVLFGGMVAATYVQIVKAVLV 191

Query: 186 LSGTSFMAFMVLKHFGFSTEAMFASAVAVHAKGQAIMAPGGLLSNPVDAISLGLGMMFGT 245
            +  + +  + L HF F   A+F  A            PGG   +P+D +SL L +  GT
Sbjct: 192 WTAGAVLVLLALAHFSFDVGALFNKARLSSLHPAQYFVPGGYFKDPLDTLSLTLALALGT 251

Query: 246 AGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIVIGFGAIVMVG------TEPSY 299
           AGLPH++ RF+TV  A  ARKS       +  F +++I++GF A  +VG      T  S 
Sbjct: 252 AGLPHVMTRFYTVPSAVAARKSAKIGLIVMTSFAVMMILLGFSATAIVGPAAILATHSSG 311

Query: 300 RDA---TGAIIGGGNMIAVHLAQAVGGNLFLGFISAVAFATILAVVAGLALSGASAVSHD 356
             A       +GGG       A + GG L L  +SA+AFATILAVV+G+ +S AS +SHD
Sbjct: 312 NSAITLLATTLGGG-------AGSAGGELLLACVSAIAFATILAVVSGIMISSASTISHD 364

Query: 357 LYACVIRQGKATEQEEMRVSRIATLLIGLLAVLLGLMFESQNIAFLSGLVLAVAASVNFP 416
           ++  +    +  E+ ++ +++IAT++ G+ A+ L L+ ++ N+AFL GL  A+AAS N P
Sbjct: 365 IFGQLFSASRDKERRQVVIAKIATIVFGIAAMGLALLVKTFNVAFLVGLAFAIAASANLP 424

Query: 417 VLLLSMFWKGLTTRGAVCGSMAGLASAVLLVVLGPAVWVN---VLHHEKALFPYSNPALF 473
           V+L SM+W+  T RGAV   +AG  S++ LV+LGPAV      +       F  SNP LF
Sbjct: 425 VILFSMYWRRFTDRGAVAAVLAGTLSSIGLVLLGPAVIGAKGIIFKDSTPPFWLSNPGLF 484

Query: 474 SMSLAFLSAWVFSVTDSSERASEERGRYLAQFIRSMTGIGAAGASKH 520
           S+ + F++ W+ SVT S   A      + AQ +R ++G+GA  AS+H
Sbjct: 485 SIPVGFIAGWIGSVTTSQNAADTS---FDAQQLRMLSGLGAEAASEH 528


Lambda     K      H
   0.328    0.139    0.407 

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: 750
Number of extensions: 49
Number of successful extensions: 6
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: 520
Length of database: 528
Length adjustment: 35
Effective length of query: 485
Effective length of database: 493
Effective search space:   239105
Effective search space used:   239105
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: 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