GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas fluorescens GW456-L13

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= reanno::pseudo3_N2E3:AO353_05485
         (953 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832
          Length = 838

 Score =  452 bits (1163), Expect = e-131
 Identities = 275/678 (40%), Positives = 378/678 (55%), Gaps = 22/678 (3%)

Query: 277 ELPADWPSARIALANAHGLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLS 336
           EL  +     I +A+  GLHARPA ++ Q A+ F+ + ++        + +  SL  L+ 
Sbjct: 166 ELAGEEVVGHIRIAHRGGLHARPAALIRQTAQGFKSKSQLHFAG---KSATCDSLIGLMG 222

Query: 337 LGARRGQVLELIAEPSIAADALPALLRAIEEGLGEDIEPL-PTVSAQSEVIDEITDVVVA 395
           L       +++  +   A  AL ALL A+   L ED     PT  AQ             
Sbjct: 223 LAIGEQAEVQVSCQGPDAEAALQALLTALSTALAEDSHAAAPTTIAQRN----------R 272

Query: 396 PASGCVIQAVAAAPGIAIGPAHIQVLQAIDYPLRG--ESTAIERERLKTSLADVRRDIEG 453
           PA   V+  V AAPG+  GP  +  L AI  P+         +++ L  +L+ VR +IE 
Sbjct: 273 PAEAGVLHGVCAAPGLVGGP--LFHLNAISLPVDAGHHDPQQQQQVLDAALSQVRSEIER 330

Query: 454 ---LIQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQES 510
              L ++ K  A   IF  H  +L+DP L D     + QG +A  AW   ID      + 
Sbjct: 331 TLVLAKKHKDTAEEAIFAAHLALLEDPALLDAAIQTVAQGTAATHAWSQAIDVQCEVLQQ 390

Query: 511 LQDALLAERAADLRDIGRRVLAQLCGIETPSEPDQPYILVMDEVGPSDVARLDPTRVAGI 570
               LLAERA DLRD+ +RVL  L G     +     I+   E+ PSD+ +L    VAG+
Sbjct: 391 TGSTLLAERANDLRDLKQRVLRALLGDTWHYDVPAGAIVAAHELTPSDLLQLSQQGVAGL 450

Query: 571 LTARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRA 630
             A GGAT+H AI+AR  G+P +V  G+ +L    G P++LD   GRL +   A  L   
Sbjct: 451 CMAEGGATSHVAILARGKGLPCMVALGSTLLDQQQGQPVVLDADGGRLELTPSAERLADV 510

Query: 631 AEERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTEL 690
            + +  ++QR     AQ H PALTTDG  +EV AN+  S     A+  GA+G+GLLRTE 
Sbjct: 511 RQLQQQQQQRRAEQQAQAHTPALTTDGLRIEVAANVASSTEAADALANGADGVGLLRTEF 570

Query: 691 IFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRG 750
           +F+    APDE  Q   Y+ VLD +  + +++RT+DVGGDK L Y P+  E NP LG+RG
Sbjct: 571 LFVDRHTAPDEQEQHHAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRG 630

Query: 751 IRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEIPVADL- 809
           IRL   RP++++ QLRALL        RI+ PMV  VDE        + L  E+ +A   
Sbjct: 631 IRLAQARPELLDQQLRALLHLRPLSRCRILLPMVTEVDELLHIHQRLDALCGELGLAQRP 690

Query: 810 QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQL 869
           +LG+MIEVP+AALLA  LA+  DF S+GTNDL+QYTLA+DR H  L+A+ D LHPA+L+L
Sbjct: 691 ELGVMIEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRL 750

Query: 870 IDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQ 929
           I  T   A  H +WVGVCG LA+DPLA PVL+GLGV ELSVS   +GE+K RVR L  ++
Sbjct: 751 IAQTCAGAAQHNRWVGVCGALASDPLATPVLIGLGVSELSVSPVQVGEIKDRVRHLDASE 810

Query: 930 VKHLAQLALAVGSANEVR 947
            + ++Q  L + SA+ VR
Sbjct: 811 CRRISQGLLKLSSASAVR 828


Lambda     K      H
   0.319    0.135    0.383 

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: 1636
Number of extensions: 80
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 953
Length of database: 838
Length adjustment: 43
Effective length of query: 910
Effective length of database: 795
Effective search space:   723450
Effective search space used:   723450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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