Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate CA265_RS24650 CA265_RS24650 beta-phosphoglucomutase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__Pedo557:CA265_RS24650 Length = 228 Score = 172 bits (436), Expect = 5e-48 Identities = 91/214 (42%), Positives = 129/214 (60%), Gaps = 2/214 (0%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 +KA +FDLDGV+ DTA YH+ AWK +A + F + NE+LKG+SR ESL IL +GG Sbjct: 16 IKACLFDLDGVLVDTAVYHYKAWKRLANTMGFDFTEEQNEQLKGVSRVESLNKILAWGGI 75 Query: 61 ETKYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSSRNAP 120 E T++EK EL KN Y +I+K+TP ++LPG L + K+ L S+S+N+ Sbjct: 76 EK--TDSEKDELAGLKNSWYVDMITKMTPAEVLPGTVDFLTAIHKAGYKLALGSASKNSG 133 Query: 121 KILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGISAIKS 180 IL + + F IVD + K KPDP++FL A +L +P +C EDA AG+ A K Sbjct: 134 IILEKTDLAHFFDKIVDGNMVTKSKPDPEVFLKGAELLGFAPDECVVFEDAVAGVEAAKR 193 Query: 181 AGMFAVGVGQGQPMLGADLVVRQTSDLTLELLHE 214 GM A+G+G+ + AD+VV LT++ L E Sbjct: 194 GGMKAIGIGEKSVLTQADVVVSGLDKLTVKDLEE 227 Lambda K H 0.319 0.136 0.390 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: 142 Number of extensions: 8 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: 226 Length of database: 228 Length adjustment: 22 Effective length of query: 204 Effective length of database: 206 Effective search space: 42024 Effective search space used: 42024 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate CA265_RS24650 CA265_RS24650 (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.20536.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-74 235.3 0.0 3.2e-74 235.0 0.0 1.1 1 lcl|FitnessBrowser__Pedo557:CA265_RS24650 CA265_RS24650 beta-phosphoglucom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS24650 CA265_RS24650 beta-phosphoglucomutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.0 0.0 3.2e-74 3.2e-74 1 187 [] 16 202 .. 16 202 .. 1.00 Alignments for each domain: == domain 1 score: 235.0 bits; conditional E-value: 3.2e-74 TIGR01990 1 lkaviFDlDGvitdtaeyhylawkkladelgiefdeelnesLkGvsReesleailkkakkkyseeeke 68 +ka +FDlDGv++dta yhy+awk+la+ +g f+ee+ne+LkGvsR esl++il ++ + +++ek lcl|FitnessBrowser__Pedo557:CA265_RS24650 16 IKACLFDLDGVLVDTAVYHYKAWKRLANTMGFDFTEEQNEQLKGVSRVESLNKILAWGGIEKTDSEKD 83 799***************************************************************** PP TIGR01990 69 elaerknekYvellkeltpedvlpgikelleelkkkkikialasasknaklvleklelkdkfdaivda 136 ela kn+ Yv++++++tp++vlpg +++l+ ++k+++k+al+saskn+ ++lek +l++ fd ivd+ lcl|FitnessBrowser__Pedo557:CA265_RS24650 84 ELAGLKNSWYVDMITKMTPAEVLPGTVDFLTAIHKAGYKLALGSASKNSGIILEKTDLAHFFDKIVDG 151 ******************************************************************** PP TIGR01990 137 aevkkgkPdPeiFlaaaeklgvspeecigieDaeaGieaikaagilavgvg 187 + v+k+kPdPe+Fl++ae lg +p+ec+++eDa aG+ea+k++g+ a+g+g lcl|FitnessBrowser__Pedo557:CA265_RS24650 152 NMVTKSKPDPEVFLKGAELLGFAPDECVVFEDAVAGVEAAKRGGMKAIGIG 202 *************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (187 nodes) Target sequences: 1 (228 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.46 // [ok]
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