GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manP in Rhodobacter johrii JA192

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate WP_108222994.1 C8J29_RS00715 PTS fructose transporter subunit EIIBC

Query= BRENDA::O31645
         (650 letters)



>NCBI__GCF_003046325.1:WP_108222994.1
          Length = 581

 Score =  387 bits (995), Expect = e-112
 Identities = 211/468 (45%), Positives = 303/468 (64%), Gaps = 22/468 (4%)

Query: 1   MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60
           +K++AITSCP GIAHT+MAAE L + A   G  I+VETQG +G +++LT  EI  AD +I
Sbjct: 119 LKIVAITSCPTGIAHTFMAAEGLVEGARAQGHQIRVETQGSVGAQDELTAAEIAAADLVI 178

Query: 61  IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQ 120
           IAAD+ V+  RF GK+L     +  I     LI+KA   +  +   +  SE+   + KK 
Sbjct: 179 IAADKQVDLGRFGGKRLFLSPTKPAITDGAGLIRKA-QAEARMQAGSASSEAAQPEAKKV 237

Query: 121 NPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSF----WKTIEQIGS 176
             +Y+HLM GVSFM+PF+V GGLLIA+A  LGG      + + +D +      T+ QIG+
Sbjct: 238 G-VYKHLMTGVSFMLPFVVAGGLLIAIAFALGG------IYVYEDQYAGTLGHTLFQIGA 290

Query: 177 -ASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAG 235
             +F+ M+P LAGYIA+SIAD+PGL PGM GG IA T        GAGFLGGI+AGF+AG
Sbjct: 291 KGAFTLMVPALAGYIAWSIADRPGLAPGMTGGVIAGT-------IGAGFLGGIVAGFIAG 343

Query: 236 YAALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMK 294
           Y  LW+ + +K+PK +Q + P++I+P+  + + GL   +++G P A++ A++T +L GM+
Sbjct: 344 YGVLWLNRAIKLPKTLQGLKPVLILPLLGTALTGLLMYYVVGEPTARLLATITAFLQGMQ 403

Query: 295 GSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIA 354
           G+S+ LL L+LG M++ DMGGPVNK A+ F + +I     E M  +  A  +PPI L +A
Sbjct: 404 GTSAALLGLLLGGMMAVDMGGPVNKAAYAFATTLIAANVLEPMAAVMCAGMVPPIALAVA 463

Query: 355 TFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIG 414
             L   +F   +RE G AAF +GL  +TEGAIPFAA+DPLRVIPS++AGS     I M  
Sbjct: 464 CRLLPARFTPEEREAGNAAFVLGLAFVTEGAIPFAARDPLRVIPSLIAGSAVAGAICMAL 523

Query: 415 NVGDRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLKKDI 461
            V  RV HGG  ++ +  AV ++  F IA++AG+ V+ L + ++K+ +
Sbjct: 524 GVAQRVPHGGVFVLPIPNAVTNLTGFGIALVAGTAVSVLALALVKRRV 571


Lambda     K      H
   0.319    0.137    0.386 

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: 851
Number of extensions: 38
Number of successful extensions: 5
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: 650
Length of database: 581
Length adjustment: 37
Effective length of query: 613
Effective length of database: 544
Effective search space:   333472
Effective search space used:   333472
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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