Aligments for a candidate for fruI in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruI in Pseudomonas putida KT2440

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate PP_0793 PP_0793 Phosphotransferase system, fructose-specific EI/HPr/EIIA components

Query= reanno::WCS417:GFF780
         (952 letters)



>lcl|FitnessBrowser__Putida:PP_0793 PP_0793 Phosphotransferase
           system, fructose-specific EI/HPr/EIIA components
          Length = 950

 Score = 1439 bits (3725), Expect = 0.0
 Identities = 741/950 (78%), Positives = 825/950 (86%), Gaps = 2/950 (0%)

Query: 1   MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI 60
           MLEL  EQI+MGQ A DK+ AL LLA++LVADGLVAEGYL GLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELANEQIAMGQKAADKAEALRLLADRLVADGLVAEGYLQGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTP+TRD V++TGVRLLQFPEGVDWGDGQ+VYLAIGIAA+SDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPQTRDLVYATGVRLLQFPEGVDWGDGQMVYLAIGIAARSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DL +ALRRA SAEALLKLLQGAPQ LALDAQ++GL V A+DF+EL WRGARLL++ADCV 
Sbjct: 121 DLAEALRRASSAEALLKLLQGAPQALALDAQLVGLNVPAEDFDELAWRGARLLQRADCVD 180

Query: 181 NGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASLGE 240
           +GFAAVLQQ + LPLG+GLWWLHSE+ V++PGLAF+TP +P+RY  QPLNGLFCLASLG 
Sbjct: 181 SGFAAVLQQAEPLPLGEGLWWLHSERQVRQPGLAFITPQQPLRYRDQPLNGLFCLASLGA 240

Query: 241 AHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPA 300
           AH+ LLERLC +LIEGRGQ L +ATSSRAVLEVLGGE+P DWP+AR+ LAN HGLHARPA
Sbjct: 241 AHEALLERLCEVLIEGRGQVLYQATSSRAVLEVLGGEVPADWPSARVVLANPHGLHARPA 300

Query: 301 KILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPA 360
           K+LAQLAK F+G++RVR+VD    AVSVKSLSKLLSLGARRGQ LE +AEPSIA DALP 
Sbjct: 301 KVLAQLAKGFEGEIRVRLVDSAQPAVSVKSLSKLLSLGARRGQALELVAEPSIAADALPV 360

Query: 361 LLAAVEEGLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVL 420
           LLAA+E+GLGE+VEPLP  SV P   D+   L AP AGS++Q + AAPGIA GPAH+ V 
Sbjct: 361 LLAAIEQGLGEEVEPLPQ-SVAPIADDVPEVLQAPAAGSRIQGVGAAPGIASGPAHVCVE 419

Query: 421 QVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTD 480
           + FDYPLRGESCA+ER++L  ALA V  ++Q L+ RS  KAI EIFVTHQEML DP LTD
Sbjct: 420 REFDYPLRGESCALERQKLREALATVNGELQALVLRSD-KAIGEIFVTHQEMLADPALTD 478

Query: 481 EVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ 540
           +V+ RL QGESA AAWM+VIEAAA+QQE+L DALLAERAADLRDIGRRVLAQLCGV+   
Sbjct: 479 DVEQRLAQGESAAAAWMAVIEAAARQQEALHDALLAERAADLRDIGRRVLAQLCGVQAQV 538

Query: 541 EPSEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVL 600
           EP +PY+LVM EVGPSDVARLDP RVAGI+TA+GGATAHSAIVARALGIPA+VGAG ++L
Sbjct: 539 EPEQPYVLVMTEVGPSDVARLDPNRVAGIVTAQGGATAHSAIVARALGIPAVVGAGASIL 598

Query: 601 LLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVE 660
           LL +GTPLLLDGQRG + V   A  LQRA  ERD REQRLQAA A R EPA+TRDGHAVE
Sbjct: 599 LLESGTPLLLDGQRGVVSVAPPADELQRALAERDLREQRLQAAWANRFEPAITRDGHAVE 658

Query: 661 VFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLV 720
           VFANIG+S G+A  VEQGAEG+GLLRTELIFMAHPQAPD ATQEAEYRRVLDGL GRPLV
Sbjct: 659 VFANIGDSNGIAKVVEQGAEGVGLLRTELIFMAHPQAPDVATQEAEYRRVLDGLDGRPLV 718

Query: 721 VRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMF 780
           VRTLDVGGDKPLPYWPIA EENPFLGVRG+RLTLQRPQ+ME QLRALLR+AD RPLRIMF
Sbjct: 719 VRTLDVGGDKPLPYWPIAAEENPFLGVRGVRLTLQRPQVMEDQLRALLRAADQRPLRIMF 778

Query: 781 PMVGSVDEWRAARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL 840
           PMVG V EWR AR M ERLR EIPVADLQLGIM+EVPSAALLA  LA+EVDFFS+GTNDL
Sbjct: 779 PMVGQVHEWREARAMVERLRAEIPVADLQLGIMVEVPSAALLAAQLAREVDFFSIGTNDL 838

Query: 841 TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV 900
           TQYTLAIDRGHP+LSAQADGLHPAVL LID+TVRAAHAHGKWVGVCGELAADP AV VL+
Sbjct: 839 TQYTLAIDRGHPSLSAQADGLHPAVLSLIDMTVRAAHAHGKWVGVCGELAADPQAVAVLL 898

Query: 901 GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRALVE 950
           GL VDELSVSARSI EVKA VR+     A+ LA++AL   S A VRALVE
Sbjct: 899 GLDVDELSVSARSIAEVKALVRQADHQTARALAREALQQDSAAAVRALVE 948


Lambda     K      H
   0.318    0.135    0.385 

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: 2363
Number of extensions: 80
Number of successful extensions: 4
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: 952
Length of database: 950
Length adjustment: 44
Effective length of query: 908
Effective length of database: 906
Effective search space:   822648
Effective search space used:   822648
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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 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

GapMind for catabolism of small carbon sources