GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagPcb in Shewanella oneidensis MR-1

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 200788 SO1623 PTS system, glucose-specific IIBC component (NCBI ptt file)

Query= SwissProt::O34521
         (452 letters)



>lcl|FitnessBrowser__MR1:200788 SO1623 PTS system, glucose-specific
           IIBC component (NCBI ptt file)
          Length = 499

 Score =  259 bits (663), Expect = 1e-73
 Identities = 156/465 (33%), Positives = 248/465 (53%), Gaps = 39/465 (8%)

Query: 4   FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQA--------GTAVFDHLPLIFA 55
           F Q+L ++ ++PIA+LPA G++L L    V  IPF+ +         G  +F  +P++FA
Sbjct: 27  FAQRLSQALLIPIAILPAAGVMLGL---TVSPIPFMPEVLNVLMLAVGKLIFAIMPILFA 83

Query: 56  IGIAIGISKDSNGAAGLSGAISYLMLDAATKTID-------------KTNNMAVFGGIIA 102
           + +AIG  +D  G A  +    Y ++ A    +              +T +  + GG++ 
Sbjct: 84  VAVAIGFCRDQ-GIAAFTAVFGYGVMTATLAALADLYQLPTQLVLGMETLDTGIAGGMLI 142

Query: 103 GLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGE 162
           G +  +     +  +LP    FF GRR   +L   + + L  +   +WP +   I    +
Sbjct: 143 GGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIPLAMGLGYVLAHIWPSLSLLIERVSD 202

Query: 163 WML-GLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYN-----GVTGDLARFFAKD 216
           W +     I  G++G   RLLIPLGLHH+ N  F+ + G+Y       V G++AR+ A D
Sbjct: 203 WAVYQKPAIAFGVYGALERLLIPLGLHHIWNAPFYLEVGQYQLQDAEVVRGEVARYLAGD 262

Query: 217 PTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFA 276
           P AG    G+  I M+GLPAA LA+   A  S+R   AG+M+  A  +++TG+TEPIEFA
Sbjct: 263 PQAGNLAGGYL-IKMWGLPAAALAIWRCADNSERNRVAGIMLSAAAASWLTGVTEPIEFA 321

Query: 277 FMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGIC 336
           FMF++PLL+ +H +L+GL+ F+   L I     FS G +D+ L + ++       ++G  
Sbjct: 322 FMFVAPLLFLIHVMLSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFAVLGPL 381

Query: 337 YAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDH 396
            A +Y+I+F   I A NLKTPGR   D  +   E+         ++  LGG++N+  ++ 
Sbjct: 382 TAVIYYILFRGSILAFNLKTPGRLQSDGTKGSKESL------RAIIAALGGRDNIVELNA 435

Query: 397 CATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441
           C TRLRL+V    LV++  L + GAKGV+   G+ VQ++ G   E
Sbjct: 436 CLTRLRLSVHSPELVNKVRLSQLGAKGVIVM-GKGVQIVYGTKAE 479


Lambda     K      H
   0.326    0.144    0.429 

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: 554
Number of extensions: 33
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: 452
Length of database: 499
Length adjustment: 33
Effective length of query: 419
Effective length of database: 466
Effective search space:   195254
Effective search space used:   195254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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