GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Sinorhizobium meliloti 1021

Align fructokinase; EC 2.7.1.4 (characterized)
to candidate SMc02164 SMc02164 fructokinase

Query= CharProtDB::CH_006620
         (326 letters)



>FitnessBrowser__Smeli:SMc02164
          Length = 308

 Score =  419 bits (1077), Expect = e-122
 Identities = 203/279 (72%), Positives = 234/279 (83%)

Query: 1   MILCCGEALIDMLPRDTTLGEKGFAPYAGGAIFNTAIALGRLGIPTAFFTGIADDMMGEI 60
           MI+CCGEALIDMLPR+TT GE  FAPYAGGAIFNTA+ALGRLG+PT FFTG++DDM G+I
Sbjct: 1   MIVCCGEALIDMLPRETTAGESAFAPYAGGAIFNTAVALGRLGVPTGFFTGLSDDMFGDI 60

Query: 61  LLETLKASNVDYSPCAITPRPSTIAFVKLVNGQATYAFYDEGTAGRMITTADLPDLGDDC 120
           L  TLKA+NVD++PCA  P  +T+AFVKLV+G A+YAF+DE TAGRMIT   LP LGD C
Sbjct: 61  LRATLKAANVDFAPCATLPLHTTLAFVKLVDGHASYAFFDENTAGRMITAEHLPALGDFC 120

Query: 121 EALHFGAISLIPSPCGETYEALLDREAASRVISLDPNIRPGFIKDKPSHMARIKRMAAKS 180
           EALHFGAISLIP PCG TYEAL+ RE   RVIS DPNIRPGFIKD+ +H+ R+ RMAA S
Sbjct: 121 EALHFGAISLIPEPCGSTYEALMAREHEKRVISFDPNIRPGFIKDREAHVGRMNRMAAMS 180

Query: 181 DIVKFSDEDLDWFGLQGDHDALAAHWLNHGAKLVVITKGAEGASGYTKDRKVTVPSERVT 240
           DIVKFSDEDL WFG++G HDALAA WL  G KLV+IT+GA+GA GYT   KV V SERV 
Sbjct: 181 DIVKFSDEDLAWFGMEGSHDALAAEWLKRGPKLVLITRGADGAVGYTNGHKVEVASERVE 240

Query: 241 VVDTVGAGDTFDAGILASLKMDNLLTKRQVASLDEQALR 279
           VVDTVGAGDTFDAG+LASLK +NLLTK +VASL ++A+R
Sbjct: 241 VVDTVGAGDTFDAGVLASLKFNNLLTKERVASLTDEAIR 279


Lambda     K      H
   0.319    0.137    0.410 

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: 341
Number of extensions: 7
Number of successful extensions: 1
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: 326
Length of database: 308
Length adjustment: 27
Effective length of query: 299
Effective length of database: 281
Effective search space:    84019
Effective search space used:    84019
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.

Links

Downloads

Related tools

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