Aligments for a candidate for ppa in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources