Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas fluorescens FW300-N1B4

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833
          Length = 844

 Score =  654 bits (1688), Expect = 0.0
 Identities = 388/848 (45%), Positives = 522/848 (61%), Gaps = 34/848 (4%)

Query: 4   KNLALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHAL 63
           + L L APLSG +MPL++VPD VFSS  +G+G+ IDP +  L AP  G++S++  + HA+
Sbjct: 5   QQLQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVSGHAV 64

Query: 64  SLRADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITV 123
           S+  DNG ++L+H+GLDTV L G+GF  LVEEG RVI GQ L+ FD D +A  +RSL+T+
Sbjct: 65  SITDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARSLLTL 124

Query: 124 MILTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHH 183
           M++ +G+ F      T  VE G PLL L+P +          GE    + V     + + 
Sbjct: 125 MLVVSGEPFTWLAPETGVVESGQPLLSLNPSEGAADEGIAQEGEALFSKPVT----LPNT 180

Query: 184 GGLHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSE 243
            GLHARPAA+  + A+GF++   LH     A+  SLV IM L  A  D ++V   G D+E
Sbjct: 181 NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQVSAAGADAE 240

Query: 244 AALGALLAALASATAGAPKDAPRAIAPGEP-ARPAAVAGTLAGVCASPGLASGPLARLGA 302
            A+  L   LA+       +A   +A  E  A   +    L GVCASPG A G + ++  
Sbjct: 241 VAIKTLAELLAAGCG----EAVTLMAEVETVAAQVSSLTVLRGVCASPGAAFGQVVQIAE 296

Query: 303 ISLPADDGRHRP--EEQHL--ALDQA---LQRVRDDVQGSLQQARLGGDENEAAIFSAHL 355
            +L   +    P  E +HL  AL +A   LQ++RD   G  Q          A IF AH 
Sbjct: 297 QTLEVSESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQ----------ADIFKAHQ 346

Query: 356 ALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVL 415
            LLEDPGLLD A  LID G  A  AW  A ++   + + LGN LLAERA DL D+ +RVL
Sbjct: 347 ELLEDPGLLDQALALIDAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVL 406

Query: 416 RVLLG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGL 474
           +++LG +   + +P GAI+ A ++TPS  A L      G     GGATSHVAILAR+ GL
Sbjct: 407 KLILGVEDRAMELPDGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGL 466

Query: 475 PCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQ---AD 531
           P +  L   +L L  G +V+LDA +G L+L P+   +EQ+    A R+ Q++RQQ   A+
Sbjct: 467 PAICGLPVQVLTLINGTRVLLDADKGELQLDPELAAIEQLQ---ANRQLQKQRQQYELAN 523

Query: 532 AQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNA 591
           A   A TRDG  +EI AN+AS  EA +A A G DGVGLLR+EFL+L+R  AP  +EQ + 
Sbjct: 524 AGLAARTRDGHHVEITANIASLAEAEQAMALGGDGVGLLRSEFLYLDRNHAPSHDEQAST 583

Query: 592 YQEVLDAMGQ-RKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLR 650
           Y  +  A+G  R +++RT+DVGGDK L Y+P+  E NP LG+RGI L   RP+LL  Q +
Sbjct: 584 YGAIARALGPARNLVVRTLDVGGDKPLAYVPMDRETNPFLGMRGIRLCLERPQLLRDQFK 643

Query: 651 ALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLAD 710
           A+L    L R  I+LPMV+++ ELR  R+ L E A  LG+  LP+LG+MIEVP+AAL+AD
Sbjct: 644 AILSSAGLARLHIMLPMVTQLSELRLARQLLEEEALALGLTELPKLGIMIEVPAAALMAD 703

Query: 711 QLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVG 770
             A   DF SIGTNDL+QY LAMDR H  LA + D+ HP++LRLIA T   A  HG+WVG
Sbjct: 704 LFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIATTVKAAHAHGKWVG 763

Query: 771 VCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARA 830
           VCGALAS+ LA P+L+GLGV+ELSV   L+  IK  VR++D  +C+  AQ +L L SA  
Sbjct: 764 VCGALASEKLAVPLLLGLGVDELSVSVPLIPAIKAAVREVDLLDCQAIAQQVLGLESAEQ 823

Query: 831 VRDACLQH 838
           VR+A  +H
Sbjct: 824 VREALRRH 831


Lambda     K      H
   0.319    0.136    0.390 

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: 1640
Number of extensions: 71
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: 842
Length of database: 844
Length adjustment: 42
Effective length of query: 800
Effective length of database: 802
Effective search space:   641600
Effective search space used:   641600
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