GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_0793
          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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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