GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__MR1:200788
          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:

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