Align Glucose kinase (characterized, see rationale)
to candidate SMc02835 SMc02835 glucokinase
Query= uniprot:Q8P6S9 (338 letters) >FitnessBrowser__Smeli:SMc02835 Length = 339 Score = 150 bits (380), Expect = 3e-41 Identities = 97/322 (30%), Positives = 154/322 (47%), Gaps = 8/322 (2%) Query: 11 AFPRPETFVAADVGGTHVRLALACESNDPRKPVTVLDYRKYRCADYPGLAEIMAAFFAEL 70 +FP P + D+GGT+ R AL ++ K + + R D+ + E M + Sbjct: 8 SFPFP--ILIGDIGGTNARFALLTDAYGEPKQLAPI-----RTGDFATIEEAMQKGILDK 60 Query: 71 SCAPVRRGVIASAGYALEDGRVITANLPWVLAPEQIRQQLGMQALHLVNDFEAVAYAANY 130 + R ++A AG ++ + N WV+ P+ + LG++ + ++NDFEA A A Sbjct: 61 TSVQPRSAILAVAG-PIKGDEIPLTNAGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAA 119 Query: 131 MTGNQVMQLSGPAQGAPGPALVLGPGTGLGAALWIPNGGNSVVLPTEAGHAALAAASDLE 190 V+Q+ G A +VLGPGTGLG A + + +P E GH + ++ + Sbjct: 120 PADQDVVQIGGGAVRPFHSRVVLGPGTGLGVAGLVYAQHTWIPVPGEGGHVDIGPRTERD 179 Query: 191 VALLQELRRTRTHVATEHFLSGPGLLTLYTALATLRDAPAVHATPAAVTAAALAGDDVLA 250 + L +A E L G G++ LY A+ AV A AAVT +AL+G D A Sbjct: 180 FRIWPFLEPIEGRMAGEQILCGRGIMNLYRAVCAANGEEAVLADQAAVTTSALSGADAAA 239 Query: 251 HEALQTFCGFMGSVVGDMMLLYGVRSGVYLAGGFLPQIADFIARSDFAARLLDKGPLRPA 310 E + F ++G V GDM L++ R GV+LAGG +I + + +F A DK P Sbjct: 240 VETVSLFATYLGRVAGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSAL 299 Query: 311 LEQVPVRIVEHGQLGVIGAASW 332 + +P V H + G A++ Sbjct: 300 MRTIPTFAVIHPMAALSGLAAF 321 Lambda K H 0.321 0.136 0.407 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: 254 Number of extensions: 13 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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