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

GapMind for catabolism of small carbon sources

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

Align PTS system, IIABC components (characterized, see rationale)
to candidate AO356_17535 AO356_17535 PTS N-acetyl-D-glucosamine transporter

Query= uniprot:Q836Y6
         (722 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_17535
          Length = 571

 Score =  206 bits (525), Expect = 2e-57
 Identities = 171/565 (30%), Positives = 263/565 (46%), Gaps = 103/565 (18%)

Query: 11  QKFGKALMVVVAVMPAAGLMISIGKSLPLIDPNLGLLVTTGGVLESIGWAIIGNLHLLFA 70
           Q+ G+ALM+ +A++P AGL++ +G +  L+D           ++   G AI  NL ++FA
Sbjct: 10  QRLGRALMLPIAILPIAGLLLRLGDT-DLLDI---------AIIHDAGQAIFANLAMIFA 59

Query: 71  LAIGGSWAKDRAGGAFAAGISFVLINRITGAIFGVTNEMLADEQAFTHTLFGTKIMVKGF 130
           + I   +A+D  G A  AG    L+   T                               
Sbjct: 60  IGIAVGFARDNNGTAGLAGAIGYLVMIAT------------------------------- 88

Query: 131 FTSVLEAPALNMGVFVGIIAGFVGAMAYNKYYNYRKLPDALSFFNGKRFVPFVVILWSTI 190
              VL+A ++NMG+  GII+G +    YN++ +  KLP+ L+FF G+RFVP V    +  
Sbjct: 89  -LKVLDA-SINMGMLAGIISGLLAGALYNRFKDI-KLPEYLAFFGGRRFVPIVTGFSAVG 145

Query: 191 VSIALALIWPNIQAGINNFGLWIAQSQDSAPILAPFLYGTLERLLLPFGLHHMLTIPINY 250
           + +   LIWP IQ GIN FG  + +S         F++G   RLL+  GLHH+L      
Sbjct: 146 LGVVFGLIWPPIQQGINGFGALLMESGS----FGAFVFGVFNRLLIVTGLHHILN----- 196

Query: 251 TQLGGTYEILSGAQAGTQVFGQ--DPLWLAWATDLVNLKGAGDMSKYQFVLENWTPARFK 308
                             +FG   DP   A  T  ++   AGD    QF+   +    F 
Sbjct: 197 -------------NMAWFIFGSFTDPATGAVVTGDLSRYFAGDPKGGQFMTGMFPVMLFG 243

Query: 309 VGQMIGSSGILMGMALAMYRNVDADKKAKYKSMYFSAALAVFLTGVTEPLEFMFMFAAVP 368
                     L    LAMYRN    ++     +  S AL  FLTGVTEP+EF FMF A  
Sbjct: 244 ----------LPAACLAMYRNALPQRRKVMGGILLSMALTSFLTGVTEPIEFAFMFLAPL 293

Query: 369 LYVIYAVIQGAAFAMADILPLRV---HSFGNIELLTRTPLAIKAGLGGDLINFVLMVIIF 425
           L++++A++ G + A+ ++L + +    S G I+++    L       G L+  V + + +
Sbjct: 294 LFLVHALLTGVSMAVTNLLGIHLGFTFSGGFIDMV----LGWGKSTNGWLV--VPVGLAY 347

Query: 426 GVVTYFLANFLIKKFNYATPGRNGNYDNDNSEEIASGAAGSGVVDQQIAQIVYLLGGKQN 485
             + Y + +F I++F+  TPGR         EE+ +G   +   +Q+ A  +  LGG  N
Sbjct: 348 AAIYYLVFDFCIRRFDLKTPGR---------EEVPAGDKPAIAENQRAAAYIQALGGADN 398

Query: 486 IKEVDACMTRLRVSVKDREKVGSEEAWKRAGAMGLIVKDNG--VQAVYGPKADVLKSDIE 543
           +  + AC TRLR+ + DR K  S+   K  GAM ++   NG  +Q V GP AD +  +I 
Sbjct: 399 LITIGACTTRLRLDMVDRNK-ASDAQLKALGAMAVVRPGNGGSLQVVVGPMADSIADEIR 457

Query: 544 DLLASGVDIPEPVIAE-STAGVPTT 567
             + S +    PV A    A  PTT
Sbjct: 458 LAVPSSL---RPVTAPVPNAPAPTT 479


Lambda     K      H
   0.322    0.138    0.404 

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: 955
Number of extensions: 53
Number of successful extensions: 7
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: 722
Length of database: 571
Length adjustment: 38
Effective length of query: 684
Effective length of database: 533
Effective search space:   364572
Effective search space used:   364572
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 (21.9 bits)
S2: 54 (25.4 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