Align beta-Phosphoglucomutase (EC 5.4.2.6) (characterized)
to candidate WP_027698533.1 TT13_RS02545 beta-phosphoglucomutase
Query= BRENDA::P71447 (221 letters) >NCBI__GCF_000691805.2:WP_027698533.1 Length = 223 Score = 164 bits (416), Expect = 9e-46 Identities = 88/192 (45%), Positives = 122/192 (63%), Gaps = 9/192 (4%) Query: 3 KAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK 62 K FD+DGV+ DTA +H AW+ +A+E+G + + E LKG+ R SL IL D Sbjct: 8 KGFAFDMDGVLADTARFHAIAWRQIADEVGTTWTE-ELAEALKGIDRMGSLDLILQAGDV 66 Query: 63 KVSAEEF-----KELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASK 117 AE++ + LA +KNDNY +I ++ AD PGI L +L + K+++ASASK Sbjct: 67 ---AEQYDLPAREALANKKNDNYRALISKLTSADALPGIFPFLDELLAAGYKMSIASASK 123 Query: 118 NGPFLLEKMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQA 177 N PF++E++ + YFDAI DPA V A KP P IF AAA A+ +AP +GLEDS AGI++ Sbjct: 124 NAPFIVERLGMEKYFDAIVDPASVKAGKPDPAIFAAAAAAIDLAPEVVVGLEDSAAGIKS 183 Query: 178 IKDSGALPIGVG 189 I D+G L IG+G Sbjct: 184 INDAGELSIGIG 195 Lambda K H 0.316 0.135 0.377 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: 159 Number of extensions: 6 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: 221 Length of database: 223 Length adjustment: 22 Effective length of query: 199 Effective length of database: 201 Effective search space: 39999 Effective search space used: 39999 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 45 (21.9 bits)
Align candidate WP_027698533.1 TT13_RS02545 (beta-phosphoglucomutase)
to HMM TIGR01990 (pgmB: beta-phosphoglucomutase (EC 5.4.2.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01990.hmm # target sequence database: /tmp/gapView.2751933.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01990 [M=187] Accession: TIGR01990 Description: bPGM: beta-phosphoglucomutase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-71 226.5 0.0 1.5e-71 226.3 0.0 1.0 1 NCBI__GCF_000691805.2:WP_027698533.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000691805.2:WP_027698533.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.3 0.0 1.5e-71 1.5e-71 1 187 [] 7 195 .. 7 195 .. 0.99 Alignments for each domain: == domain 1 score: 226.3 bits; conditional E-value: 1.5e-71 TIGR01990 1 lkaviFDlDGvitdtaeyhylawkkladelgiefdeelnesLkGvsReesleailkkakk..kyseeekeela 71 +k++ FD+DGv++dta++h aw+++ade+g +++eel+e+LkG+ R+ sl+ il+ ++ +y +e+la NCBI__GCF_000691805.2:WP_027698533.1 7 IKGFAFDMDGVLADTARFHAIAWRQIADEVGTTWTEELAEALKGIDRMGSLDLILQAGDVaeQYDLPAREALA 79 79******************************************************9987779999******* PP TIGR01990 72 erknekYvellkeltpedvlpgikelleelkkkkikialasasknaklvleklelkdkfdaivdaaevkkgkP 144 ++kn++Y+ l+++lt++d lpgi +l+el ++++k+++asaskna++++e+l+++++fdaivd+a+vk gkP NCBI__GCF_000691805.2:WP_027698533.1 80 NKKNDNYRALISKLTSADALPGIFPFLDELLAAGYKMSIASASKNAPFIVERLGMEKYFDAIVDPASVKAGKP 152 ************************************************************************* PP TIGR01990 145 dPeiFlaaaeklgvspeecigieDaeaGieaikaagilavgvg 187 dP iF aaa++++++pe ++g+eD++aGi++i++ag l++g+g NCBI__GCF_000691805.2:WP_027698533.1 153 DPAIFAAAAAAIDLAPEVVVGLEDSAAGIKSINDAGELSIGIG 195 *****************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (187 nodes) Target sequences: 1 (223 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 13.12 // [ok]
This GapMind analysis is from Sep 24 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