Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

Align Fructose PTS system (E-I, HPr, and E-IIA components) (characterized)
to candidate AO353_04460 AO353_04460 PTS N-acetyl-D-glucosamine transporter

Query= reanno::azobra:AZOBR_RS32325
         (846 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04460
          Length = 838

 Score =  427 bits (1098), Expect = e-123
 Identities = 263/664 (39%), Positives = 371/664 (55%), Gaps = 21/664 (3%)

Query: 179 GLHARPATAWVETARASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVA 238
           GLHARPA    +TA    ++ Q+      A   +L+ L+ LG+   D V VS +G DA A
Sbjct: 183 GLHARPAALIRQTAHLFNSKSQLHFAGKSASCDSLIGLMGLGIGEQDEVQVSCKGADAKA 242

Query: 239 ALARMKATITRLTAREKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVL 298
           AL   +A +  L+     D+ AAA     P+   T       + G+ A+PGL  GP+  L
Sbjct: 243 AL---QALLNALSTAVNDDSHAAAP---TPIAQRTRTAEAGVLNGVCAAPGLVGGPLFQL 296

Query: 299 PRAAVSVPDEPVP--LIEGGDRLHEALSLTRQNLKALADDTARRLGPSEAAIFAAQAEIL 356
             AA+ +P++       E    L  AL   R  ++       +     E  IFAA   +L
Sbjct: 297 --AAIPLPEDTGKHNAEEQLQALDRALEQVRSEIRETLSHAKKHKHTEEEQIFAAHLALL 354

Query: 357 NDTDLVTLACQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARI 416
            D  L+  A Q + +G     +W Q++E     L  L NP+LA RA DLRD+ QRVL  +
Sbjct: 355 EDPALLEAAIQSIDQGSAATHAWSQSIEAQCEVLQQLGNPLLAERANDLRDLRQRVLRAL 414

Query: 417 DPALRTGGAPDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGL 476
              L      D+P    I+ A +L+PSD   L    V GL  A+GG TSH AILAR  GL
Sbjct: 415 ---LGQDWHYDVP-AGAIVAAHELTPSDLLQLSQQGVAGLCMAEGGATSHVAILARGKGL 470

Query: 477 PAMVAGGAALMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGL 536
           P +VA  A+L++   G   +LD   GRL L+P +  +            R+  ++A+   
Sbjct: 471 PCLVALSASLLQQPQGQSVVLDADGGRLELTPDSQRLEQVAQAQREHLQRRERQQAQAHT 530

Query: 537 PARTRDGHEVEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRG 596
           PA TRDG  +E+ ANV   ++ A AL  GA+ VGL+RTEFLF++R  AP E EQ + Y+ 
Sbjct: 531 PAHTRDGLRIEVAANVASSNEAADALKGGADGVGLLRTEFLFVDRQTAPDEQEQRQAYQA 590

Query: 597 MLTALEGRPLIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYR 656
           +L A+  + +I+R +D+GGDKQ+ +L LP E NP LG+RG R+   RPELL+ QLRAL +
Sbjct: 591 VLDAMGDKSVIIRTIDVGGDKQLDYLPLPAEANPVLGLRGIRMAQVRPELLDQQLRALLQ 650

Query: 657 AAKDGGAKDGGALSIMFPMITALGEVQALRAACERIRAELD-APAVPLGIMVEVPAAAIQ 715
            +     +      I+ PM+T + E+  +R   + + AEL     + LG+M+EVPAAA+ 
Sbjct: 651 VSPLQRCR------ILLPMVTEVDELLYIRQRLDALCAELALTQRLELGVMIEVPAAALL 704

Query: 716 ADVLARHVDFFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRW 775
           A+ LA H DF SIGTNDL+QY LA+DR H  LAA  D+LHPA+LRLI  T  GA +H RW
Sbjct: 705 AEQLAEHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCIGAAKHQRW 764

Query: 776 VGVCGGIAGDPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETA 835
           VGVCG +A DP    +L GLG+ ELS++P  +  +K+R+R  D +  +  +   L+  +A
Sbjct: 765 VGVCGALASDPLATPVLIGLGISELSVSPPQVGEIKERVRQLDAADCRRFSATLLNLSSA 824

Query: 836 DAVR 839
            AVR
Sbjct: 825 TAVR 828


Lambda     K      H
   0.319    0.134    0.387 

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: 1511
Number of extensions: 74
Number of successful extensions: 8
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: 846
Length of database: 838
Length adjustment: 42
Effective length of query: 804
Effective length of database: 796
Effective search space:   639984
Effective search space used:   639984
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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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 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