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

GapMind for catabolism of small carbon sources

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

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 AO353_15995 AO353_15995 PTS mannose transporter subunit IIC

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15995
          Length = 844

 Score =  639 bits (1647), Expect = 0.0
 Identities = 381/841 (45%), Positives = 516/841 (61%), Gaps = 32/841 (3%)

Query: 6   LALKAPLSGPVMPLNRVPDPVFSSGTLGEGIAIDPLNDCLHAPCAGLVSHLARTRHALSL 65
           L L APLSG +MPL+ VPDPVF+S  +G+G+ IDP +  L AP AG+VS+L  + HA+S+
Sbjct: 7   LQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHSGHAISI 66

Query: 66  RADNGAELLLHVGLDTVQLQGEGFEALVEEGARVIEGQPLLRFDLDRVARGSRSLITVMI 125
             D+G ++LLH+GLDTV L+G+GF ALVE+G RV  GQPL+ FD D VA  +RSL+T+M+
Sbjct: 67  TDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARSLLTLML 126

Query: 126 LTNGDGFQVRPLTTNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHGG 185
           + +G+ F +    +  V    P+L+LS        A    GE    + V     + +  G
Sbjct: 127 VVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEE-GEALFSKPVH----LPNPNG 181

Query: 186 LHARPAALLRKTAQGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEAA 245
           LHARPAA+  + A+GF++   LH     A+  SLV IM L     D ++V   GED+E A
Sbjct: 182 LHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELA 241

Query: 246 LGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLAGVCASPGLASGPLARLGAISL 305
           +  L   LA    G        +AP   A+  +    L GVCAS G A G + ++   +L
Sbjct: 242 ISTLAQLLADG-CGEAVTPVAVVAPVVEAQEVSTK-LLRGVCASAGSAFGYVVQVAERTL 299

Query: 306 P----ADDGRHRPEEQHLAL---DQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALL 358
                A D +   E    AL    QALQR+RD+  G          E +A IF AH  LL
Sbjct: 300 EMPEFAADQQLERESLERALMHATQALQRLRDNAAG----------EAQADIFKAHQELL 349

Query: 359 EDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLRVL 418
           EDP LL+ A  LI +G  AA AW+ A +A   + ++LG+ LLAERA DL D+ +RVL+++
Sbjct: 350 EDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLI 409

Query: 419 LG-DTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCL 477
           LG       +P  AI+ A ++TPS  A L      G     GGATSHVAILAR+ GLP +
Sbjct: 410 LGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAV 469

Query: 478 VALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQAD---AQR 534
             L   +L L  G +V+LDA +G L L P    +EQ+    A+R++QR+R Q +   A R
Sbjct: 470 CGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLH---AKRQQQRQRHQHELENAAR 526

Query: 535 EALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQE 594
            A+TRDG   E+ ANVAS  E  +A + GA+G+GLLR+EFL+ +R  AP  +EQ   Y  
Sbjct: 527 AAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSA 586

Query: 595 VLDAMG-QRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALL 653
           +  A+G QR +++RT+DVGGDK L Y+P+  E NP LG+RGI L   RP+LL +Q RA+L
Sbjct: 587 IARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAIL 646

Query: 654 RVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLA 713
               L R  I+LPMVS++ ELR  R  L E A  LG+  LP+LG+MIEVP+AAL+AD  A
Sbjct: 647 SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFA 706

Query: 714 EHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCG 773
              DF SIGTNDL+QY LAMDR H  LA + D+ HP++LRLIA T   A  HG+WVGVCG
Sbjct: 707 PEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCG 766

Query: 774 ALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVRD 833
           ALAS+ LA P+L+GLGV+ELSV   L+  IK  +R+++ ++C+  A  +L L SA  VR+
Sbjct: 767 ALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVRE 826

Query: 834 A 834
           A
Sbjct: 827 A 827


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: 1662
Number of extensions: 77
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