GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Sinorhizobium meliloti 1021

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate SMc02880 SMc02880 hypothetical protein

Query= reanno::SB2B:6938110
         (299 letters)



>FitnessBrowser__Smeli:SMc02880
          Length = 303

 Score =  144 bits (363), Expect = 2e-39
 Identities = 102/295 (34%), Positives = 148/295 (50%), Gaps = 10/295 (3%)

Query: 7   DLGGTKIELVALGEDGSELFR-KRIATP-REYQGTLNAVVTLVNEAEATLGTQGSLGIGI 64
           D+GG+ I+  A+      +F   R ATP  ++   + A+ ++++EA    G    + I I
Sbjct: 6   DIGGSAIK-GAITHSPERIFPLPRRATPLTDFGRFVEAMESVLDEAG---GLPERVAISI 61

Query: 65  PGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAAGKRV 124
            GVI P T  +K AN   I+G  L  +L A L+  V +ANDA+CFA++EA  GA  G R+
Sbjct: 62  TGVIDPETRRIKCANIPCIDGRELVAELEAALHLPVVIANDADCFALAEAGVGAGRGHRI 121

Query: 125 VFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNP----LPWMRPDEFNTTECFCGNKDC 180
           VFGAILGTG G GL  DGR+     G  GEWGH P         P       C CG   C
Sbjct: 122 VFGAILGTGVGGGLVIDGRLINADGGFAGEWGHGPAVAAAAGHPPIAIPAFPCGCGQSRC 181

Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240
           ++T     G  R      G A +  +I+     G+  A    D ++D ++  LA VIN+ 
Sbjct: 182 VDTVGGARGLERLHETVHGKALSSHDIIEGWQNGNAEAARTIDVFVDLVSSPLALVINIT 241

Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWL 295
               + +GGG+SN +A+ A +   +   ++ R  R  VV+       G+ GAA L
Sbjct: 242 GATIVPVGGGLSNAEALLAEIDRAVRARILRRFDRPLVVRGECRVEPGLIGAALL 296


Lambda     K      H
   0.320    0.139    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: 291
Number of extensions: 19
Number of successful extensions: 2
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: 299
Length of database: 303
Length adjustment: 27
Effective length of query: 272
Effective length of database: 276
Effective search space:    75072
Effective search space used:    75072
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 (21.8 bits)
S2: 48 (23.1 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