GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagPcb in Shewanella amazonensis SB2B

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= SwissProt::O34521
         (452 letters)



>lcl|FitnessBrowser__SB2B:6936959 Sama_1133 PTS system,
           glucose-specific IIBC component (RefSeq)
          Length = 485

 Score =  269 bits (687), Expect = 2e-76
 Identities = 163/461 (35%), Positives = 246/461 (53%), Gaps = 34/461 (7%)

Query: 4   FLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFV-----YQAGTAVFDHLPLIFAIGI 58
           F Q+L ++ ++PIA+LPA G+++ +    +  IP V        G  +FD +P++FAI +
Sbjct: 22  FAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAIAV 81

Query: 59  AIGISKDSNGAAGLSGAISYLMLDAATKTIDK-------------TNNMAVFGGIIAGLI 105
           AIG  +D  G A  S A  Y +L +      K             T +  + GG++ G I
Sbjct: 82  AIGFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGGI 140

Query: 106 AGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWML 165
                   +  +LP    FF GRR  P++   + ++LA +   +WPP+   I    +W +
Sbjct: 141 TCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWAV 200

Query: 166 GLG-GIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNG----VTGDLARFFAKDPTAG 220
                I  G +G+  RLL+PLGLHH+ N  F+ + G+Y      V G++AR+FA DP+AG
Sbjct: 201 YQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHDGEIVRGEMARYFAGDPSAG 260

Query: 221 TYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFL 280
               G+  I M+GLPAA LA+   A  ++R   AG+M+  A  +++TG+TEPIEFAF+F+
Sbjct: 261 NLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLFV 319

Query: 281 SPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAV 340
           +PLLY  HA+LTGL+  I   L +     FS G +D+VL +  +     +  +G     +
Sbjct: 320 APLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTFVI 379

Query: 341 YFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATR 400
           Y+I+F   I A NLKTPGR + D        T Q  N   ++  LGG  N+  +  C TR
Sbjct: 380 YYILFRASILAFNLKTPGRFEAD--------TGQKRNLIAIVSALGGGGNIADLSACLTR 431

Query: 401 LRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441
           LR++V D + VD   L   GAKGV+   G  VQ++ G   E
Sbjct: 432 LRISVADPSQVDRQRLMSLGAKGVIVV-GSGVQLVFGTKAE 471


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: 531
Number of extensions: 25
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: 485
Length adjustment: 33
Effective length of query: 419
Effective length of database: 452
Effective search space:   189388
Effective search space used:   189388
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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