Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2C3

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter

Query= reanno::pseudo5_N2C3_1:AO356_07335
         (954 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17540
          Length = 837

 Score =  455 bits (1171), Expect = e-132
 Identities = 278/673 (41%), Positives = 384/673 (57%), Gaps = 30/673 (4%)

Query: 286 RIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVL 345
           ++ +A+  GLHARPA ++ Q A+ F    ++        + S  S+  ++ L       +
Sbjct: 175 QVRIAHRGGLHARPAALVRQTAQGFKSRSQLHF---SGKSASCDSVMGMMGLAITEQAQV 231

Query: 346 EFIAEPSIANDALPALLAAIEEGLGEEVEP-LPPPSAPRETVMAEVATVMLAPESGSLIQ 404
                 S A  AL ALL  +   L EE     PPP  PR              E G ++ 
Sbjct: 232 HVSCRGSDAEAALQALLTTLSTALVEEAHASAPPPEPPRANA-----------EEG-VLH 279

Query: 405 AVAAAPGIAIGPAHIQVLQAIDYP--LRGESAAIERERLQNALNQVRSDIQGLIERAKAK 462
            V AAPG+  GP  +  L  I  P  + G +   +R+RL +AL QVR +I   +E A+A+
Sbjct: 280 GVCAAPGLVTGP--LVRLSGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARAR 337

Query: 463 AIRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAE 519
             R+   IF  H  +L+DP L D  D  ++ G +A  AW   I+   +  + L   LLAE
Sbjct: 338 QHRDEEAIFSAHLALLEDPVLLDAADLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAE 397

Query: 520 RAADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGAT 579
           RA DLRD+ +RVL  L G     +     I+   E+ PSD+ +L    VAG+    GGAT
Sbjct: 398 RANDLRDLRQRVLRVLLGEAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGAT 457

Query: 580 AHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTRE 639
           +H AI+AR  G+P LV  G  +L    G +++LD   GRL + P   T++R  + R  + 
Sbjct: 458 SHVAILARGKGLPCLVALGDELLAQEQGQAVVLDADGGRLELTP---TVERLAQVRQAQT 514

Query: 640 QRLKVAAEQR---HEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAH 696
           +R  + A+Q+   H PA T DG  VEV AN+  SA    ++  GA+G+GLLRTE +F+  
Sbjct: 515 RRTALRAQQQSLAHTPARTVDGVEVEVAANVASSAEAGESLANGADGVGLLRTEFLFVDR 574

Query: 697 SQAPDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTL 756
             APDE  Q   Y+ VL+ +  +P+++RT+DVGGDK L Y P+  E NP LG+RGIRL  
Sbjct: 575 HTAPDEEEQRQAYQAVLEAMGDKPVIIRTIDVGGDKQLDYLPLPSEANPVLGLRGIRLAQ 634

Query: 757 QRPQVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIM 815
            RP +++ QLRALL++      RI+ PMV  VDE    R   + L  E+ +++  QLG+M
Sbjct: 635 VRPDLLDQQLRALLQTRPLDRCRILLPMVTEVDELLHIRKRLDALGSELGLSERPQLGVM 694

Query: 816 IEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITV 875
           +EVP+AALLA  LA+  DF S+GTNDL+QYTLA+DR H  L+A+ D LHPA+L+LI  T 
Sbjct: 695 VEVPAAALLAEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTC 754

Query: 876 RAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLA 935
             A  HG+WVGVCG LA+DPLA PVL+GLGV ELSVS   I E+K RVR L  AQ   L+
Sbjct: 755 AGAAKHGRWVGVCGALASDPLATPVLIGLGVRELSVSPPQIGEIKDRVRHLDAAQCARLS 814

Query: 936 QAALAVGSADDVR 948
              L +GSA  VR
Sbjct: 815 NELLNLGSALAVR 827


Lambda     K      H
   0.318    0.135    0.381 

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: 1529
Number of extensions: 90
Number of successful extensions: 5
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: 954
Length of database: 837
Length adjustment: 43
Effective length of query: 911
Effective length of database: 794
Effective search space:   723334
Effective search space used:   723334
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: 56 (26.2 bits)

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

Downloads

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

Related tools

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
the source code
instructions for running GapMind on your computer

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