Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate Pf1N1B4_4886 Phosphoglucomutase (EC 5.4.2.2)
Query= BRENDA::I6Y2G3 (547 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 Length = 548 Score = 652 bits (1682), Expect = 0.0 Identities = 344/549 (62%), Positives = 402/549 (73%), Gaps = 7/549 (1%) Query: 1 MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60 M +P AG+PA E LVD+P LVTAYY+ +PD Q+VAFGTSGHRGS+ +FNE H Sbjct: 1 MTLSPFAGKPAPAELLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLSFNEWH 60 Query: 61 ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120 +LAI+QAI YR AQG GPLF+G DTH LS PA SALEVLAAN V ++ D YTPT Sbjct: 61 VLAISQAICLYREAQGIDGPLFVGIDTHALSTPAGASALEVLAANGVTVMIAEGDEYTPT 120 Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180 PAISHAIL YNRGRT LADGIV+TPSHNPP GG KYNP NGGPADT T I +ANE Sbjct: 121 PAISHAILCYNRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANE 180 Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237 +L A+ + VKR+ +AL+ T RHDYL YV DL NV+D AIREA +R+G DPLGGA Sbjct: 181 LLAAKLAGVKRISYEQALKASTTHRHDYLNTYVADLINVIDFDAIREAKLRLGVDPLGGA 240 Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297 V YW IA + LDL VVN VDAT+RFMT+D DG+IRMD SS AM GLI G +E Sbjct: 241 GVRYWSAIAEHYRLDLEVVNKQVDATFRFMTVDWDGQIRMDPSSSHAMQGLI----GLKE 296 Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357 R+ +A D D DRHGIVTP GLL PN+YLAV+I+YL+ +RP W A AVGKTVVSS + Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPLWRADAAVGKTVVSSGL 356 Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417 IDRV +GR+L EVPVGFKWF DGL +LGFGGEESAGASFLR+DGSVW TDKDG+I Sbjct: 357 IDRVAKRLGRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGSVWCTDKDGLIP 416 Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477 ALLAAE+ A TG PSQ Y AL E G P R+DA A+ EQKA L++LS DQV++T+LA Sbjct: 417 ALLAAEMTARTGRDPSQAYRALTDELGEPFSVRVDAKANPEQKALLSKLSPDQVTSTQLA 476 Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537 GE I + L+ APGN A+GGLKV T N WFAARPSGTED+YKIYAESF HL ++ Sbjct: 477 GEAIQSILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFVSDDHLKQLVAE 536 Query: 538 AREVVDRVI 546 A+ +VD I Sbjct: 537 AQTLVDGAI 545 Lambda K H 0.318 0.135 0.401 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: 966 Number of extensions: 38 Number of successful extensions: 3 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: 547 Length of database: 548 Length adjustment: 36 Effective length of query: 511 Effective length of database: 512 Effective search space: 261632 Effective search space used: 261632 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 (21.7 bits) S2: 53 (25.0 bits)
Align candidate Pf1N1B4_4886 (Phosphoglucomutase (EC 5.4.2.2))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))
# 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/TIGR01132.hmm # target sequence database: /tmp/gapView.7094.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01132 [M=546] Accession: TIGR01132 Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-268 876.4 0.0 3.7e-268 876.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 Phosphoglucomutase (EC 5.4.2.2) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 Phosphoglucomutase (EC 5.4.2.2) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 876.2 0.0 3.7e-268 3.7e-268 1 545 [. 1 545 [. 1 546 [. 0.99 Alignments for each domain: == domain 1 score: 876.2 bits; conditional E-value: 3.7e-268 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilai 64 m++ p aG++a++e l+d+++lv++yy+ +pda ++q+v+fGtsGhrGs+ +fne h+lai lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 1 MTLSPFAGKPAPAELLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLSFNEWHVLAI 64 678899********************************************************** PP TIGR01132 65 aqavvevraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshail 128 +qa+ +r+aqGi Gpl++G dthals pa s+levlaan+v v++ e + ytptpa+shail lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 65 SQAICLYREAQGIDGPLFVGIDTHALSTPAGASALEVLAANGVTVMIAEGDEYTPTPAISHAIL 128 **************************************************************** PP TIGR01132 129 tynkgkkealadGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrl 192 yn+g++++ladGivitpshnpp+ GG kynp nGGpa+t++tk+ie +anell+++l+gvkr+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 129 CYNRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANELLAAKLAGVKRI 192 **************************************************************** PP TIGR01132 193 dlekalksetvkekdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldl 256 ++e+alk++t++++d+++ yv+dl +v+d++air+a+lrlGvdplGGagv yw iae+y ldl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 193 SYEQALKASTTHRHDYLNTYVADLINVIDFDAIREAKLRLGVDPLGGAGVRYWSAIAEHYRLDL 256 **************************************************************** PP TIGR01132 257 tlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGl 320 +vn++vdatfrfmt+d+dG+irmd ss +am gl+ lk+++d+af+ d+d drhGivtp+ Gl lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 257 EVVNKQVDATFRFMTVDWDGQIRMDPSSSHAMQGLIGLKERFDVAFACDPDHDRHGIVTPSGGL 320 **************************************************************** PP TIGR01132 321 lnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlld 384 l pn ylav+i+yl+++r+ w a+ avGkt+vss lidrv+ lgr+l+evpvGfkwf dGl+d lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 321 LAPNNYLAVSIDYLFQNRPLWRADAAVGKTVVSSGLIDRVAKRLGRRLYEVPVGFKWFADGLFD 384 **************************************************************** PP TIGR01132 385 gslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiya 448 gslGfGGeesaGasflrkdG+vw+tdkdG+i allaae+ta tG++p+q y +l+ ++G+p+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 385 GSLGFGGEESAGASFLRKDGSVWCTDKDGLIPALLAAEMTARTGRDPSQAYRALTDELGEPFSV 448 **************************************************************** PP TIGR01132 449 ridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsG 512 r+da a+++qka l+klspd+v++t+laG+ai + l++apGn+ aiGGlkv+t++gwfaarpsG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 449 RVDAKANPEQKALLSKLSPDQVTSTQLAGEAIQSILSHAPGNDQAIGGLKVMTENGWFAARPSG 512 **************************************************************** PP TIGR01132 513 tedvykiyaesfkgeehlkeiekeaeeivdevl 545 ted+ykiyaesf ++hlk++ ea+ +vd ++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 513 TEDIYKIYAESFVSDDHLKQLVAEAQTLVDGAI 545 *****************************9775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (548 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.07 // [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