GapMind for catabolism of small carbon sources

 

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

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 AO356_07335 AO356_07335 PTS fructose transporter subunit IIA

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07335
          Length = 954

 Score =  462 bits (1189), Expect = e-134
 Identities = 287/670 (42%), Positives = 383/670 (57%), Gaps = 21/670 (3%)

Query: 177 RARVAHHGGLHARPAALLRKTAQGFSSQAELHFA-GQVASVD--SLVGIMGLGVAEQDEV 233
           R  +A+  GLHARPA +L + A+ F  +  +    GQ ++V   SL  ++ LG      +
Sbjct: 286 RIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQVL 345

Query: 234 EVICRGEDSEAALGALLAALASATAGAPKDAPRAIAPGEPARPAAVAGTLA--------G 285
           E I     +  AL ALLAA+        +  P   AP E          LA         
Sbjct: 346 EFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLIQA 405

Query: 286 VCASPGLASGP--LARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGG 343
           V A+PG+A GP  +  L AI  P        E + L    AL +VR D+QG +++A+   
Sbjct: 406 VAAAPGIAIGPAHIQVLQAIDYPLRGESAAIERERL--QNALNQVRSDIQGLIERAKAKA 463

Query: 344 DENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAER 403
                 IF  H  +L+DP L D  D  +  G  A  AW   I+A  +  +AL + LLAER
Sbjct: 464 IRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLAER 520

Query: 404 ANDLRDLEKRVLRVLLGDTAPLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATS 463
           A DLRD+ +RVL  L G   P       I+   E+ PSD+A L     AG+  A GGAT+
Sbjct: 521 AADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATA 580

Query: 464 HVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREE 523
           H AI+AR+ G+P LV  GA +L L  G  ++LD  +GRL + PDA  L++ A +     E
Sbjct: 581 HSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQR-AKEERDTRE 639

Query: 524 QRRRQQADAQRE-ALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAA 582
           QR +  A+ + E ALTRDG  +E+ AN+      A A   GA+G+GLLRTE +F+    A
Sbjct: 640 QRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQA 699

Query: 583 PDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARP 642
           PDE  Q   Y++VLD +  R +++RT+DVGGDK L Y P+  EENP LG+RGI L   RP
Sbjct: 700 PDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRP 759

Query: 643 ELLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEV 702
           ++++ QLRALLR       RI+ PMV  VDE R  R     L  ++ +  L +LG+MIEV
Sbjct: 760 QVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMIEV 818

Query: 703 PSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGA 762
           PSAALLA  LA+  DF S+GTNDL+QY LA+DR H  L+ + D LHPA+L+LI  T   A
Sbjct: 819 PSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAA 878

Query: 763 ARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQAL 822
             HG+WVGVCG LA+DPLA PVLVGLGV+ELSV    + E+K RVR+L  A+ +  AQA 
Sbjct: 879 HAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQAA 938

Query: 823 LDLGSARAVR 832
           L +GSA  VR
Sbjct: 939 LAVGSADDVR 948


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: 1923
Number of extensions: 109
Number of successful extensions: 5
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: 842
Length of database: 954
Length adjustment: 43
Effective length of query: 799
Effective length of database: 911
Effective search space:   727889
Effective search space used:   727889
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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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:

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:

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:

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:

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