Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PP_3578 PP_3578 phosphoglucomutase
Query= BRENDA::I6Y2G3 (547 letters) >FitnessBrowser__Putida:PP_3578 Length = 545 Score = 647 bits (1670), Expect = 0.0 Identities = 341/549 (62%), Positives = 400/549 (72%), Gaps = 8/549 (1%) Query: 1 MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60 M +P AG+PA LVD+P L+TAYY+ PD AQ+VAFGTSGHRGS+L +FNE H Sbjct: 1 MTLSPLAGKPAPASVLVDIPRLLTAYYTGRPDATVAAQRVAFGTSGHRGSSLELSFNEYH 60 Query: 61 ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120 +LAI+QAI YR +G GPLFIG DTH LS PA SALEVLAAN V ++ D YTPT Sbjct: 61 VLAISQAICLYRQEKGIDGPLFIGADTHALSAPATASALEVLAANGVQVMLSKDDEYTPT 120 Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180 PA+SHAIL +NRGRT+ LADGIV+TPSHNPP GG KYNPPNGGPAD+ T I +ANE Sbjct: 121 PAVSHAILCHNRGRTQGLADGIVITPSHNPPQSGGFKYNPPNGGPADSDVTKWIEGKANE 180 Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237 +L A + VKR+ A+AL+ T RHDY+ +YV DL NV+D IR AG+R+G DPLGGA Sbjct: 181 LLAANLAGVKRMDHAQALQAPTTHRHDYVSNYVADLENVIDFDVIRGAGLRLGVDPLGGA 240 Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297 V YW IA + LDL VVN VD T+RFMT+D DG+IRMD SSP AM GLI G RE Sbjct: 241 GVRYWSAIAKHYQLDLEVVNTEVDPTFRFMTVDWDGQIRMDPSSPYAMQGLI----GLRE 296 Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357 R+ +A D D DRHGIVTPD GLL PN+YLAVAI+YL+ HRP W + AVGKTVVSS + Sbjct: 297 RFDVAFACDPDHDRHGIVTPD-GLLQPNNYLAVAIDYLFRHRPQWRSDAAVGKTVVSSGL 355 Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417 IDRV +GR L EVPVGFK+F GL +LGFGGEESAGASFLRRDGSVW TDKDG+I Sbjct: 356 IDRVTQRLGRDLYEVPVGFKFFAQGLFDGSLGFGGEESAGASFLRRDGSVWATDKDGLIP 415 Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477 ALLAAE+ A TG PSQ Y L G P R++A AD QKA L++L+ +QV +TELA Sbjct: 416 ALLAAEMTARTGRNPSQAYADLTEALGKPFATRVEAKADARQKALLSKLAPEQVKSTELA 475 Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537 GEPI L+ APGNG A+GGLKV TAN WFAARPSGTED+YKIYAESF HL + + Sbjct: 476 GEPIVQILSHAPGNGQAIGGLKVMTANGWFAARPSGTEDIYKIYAESFIDEAHLQRLVEE 535 Query: 538 AREVVDRVI 546 A+ +VD I Sbjct: 536 AQVLVDEAI 544 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: 961 Number of extensions: 31 Number of successful extensions: 4 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: 545 Length adjustment: 35 Effective length of query: 512 Effective length of database: 510 Effective search space: 261120 Effective search space used: 261120 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: 52 (24.6 bits)
Align candidate PP_3578 PP_3578 (phosphoglucomutase)
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.3632.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-269 880.5 0.0 2.1e-269 880.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3578 PP_3578 phosphoglucomutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3578 PP_3578 phosphoglucomutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 880.4 0.0 2.1e-269 2.1e-269 1 545 [. 1 544 [. 1 545 [] 1.00 Alignments for each domain: == domain 1 score: 880.4 bits; conditional E-value: 2.1e-269 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 m++ p+aG++a+++ l+d+++l+++yy+ +pda aaq+v+fGtsGhrGs+l+ +fne h+lai+qa+ +r+++ lcl|FitnessBrowser__Putida:PP_3578 1 MTLSPLAGKPAPASVLVDIPRLLTAYYTGRPDATVAAQRVAFGTSGHRGSSLELSFNEYHVLAISQAICLYRQEK 75 6789*********************************************************************** PP TIGR01132 76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnp 150 Gi Gpl+iG dthals pa s+levlaan+v+v++++ + ytptpavshail +n+g++++ladGivitpshnp lcl|FitnessBrowser__Putida:PP_3578 76 GIDGPLFIGADTHALSAPATASALEVLAANGVQVMLSKDDEYTPTPAVSHAILCHNRGRTQGLADGIVITPSHNP 150 *************************************************************************** PP TIGR01132 151 pedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaai 225 p+ GG+kynppnGGpa+++vtk+ie +anell+++l+gvkr+d ++al++ t++++d+v++yv+dl +v+d+++i lcl|FitnessBrowser__Putida:PP_3578 151 PQSGGFKYNPPNGGPADSDVTKWIEGKANELLAANLAGVKRMDHAQALQAPTTHRHDYVSNYVADLENVIDFDVI 225 *************************************************************************** PP TIGR01132 226 rkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydl 300 r aglrlGvdplGGagv yw ia++y+ldl +vn +vd+tfrfmt+d+dG+irmd sspyam gl+ l++++d+ lcl|FitnessBrowser__Putida:PP_3578 226 RGAGLRLGVDPLGGAGVRYWSAIAKHYQLDLEVVNTEVDPTFRFMTVDWDGQIRMDPSSPYAMQGLIGLRERFDV 300 *************************************************************************** PP TIGR01132 301 afgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGf 375 af+ d+d drhGivtp Gll+pn ylavai+yl++hr+qw ++ avGkt+vss lidrv++ lgr+l+evpvGf lcl|FitnessBrowser__Putida:PP_3578 301 AFACDPDHDRHGIVTP-DGLLQPNNYLAVAIDYLFRHRPQWRSDAAVGKTVVSSGLIDRVTQRLGRDLYEVPVGF 374 ****************.9********************************************************* PP TIGR01132 376 kwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyari 450 k+f +Gl+dgslGfGGeesaGasflr+dG+vw+tdkdG+i allaae+ta tG+np+q y +l++ +G+p+ +r+ lcl|FitnessBrowser__Putida:PP_3578 375 KFFAQGLFDGSLGFGGEESAGASFLRRDGSVWATDKDGLIPALLAAEMTARTGRNPSQAYADLTEALGKPFATRV 449 *************************************************************************** PP TIGR01132 451 daaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfk 525 +a a++ qka l+kl+p++v +t+laG++i l++apGng aiGGlkv+t++gwfaarpsGted+ykiyaesf lcl|FitnessBrowser__Putida:PP_3578 450 EAKADARQKALLSKLAPEQVKSTELAGEPIVQILSHAPGNGQAIGGLKVMTANGWFAARPSGTEDIYKIYAESFI 524 *************************************************************************** PP TIGR01132 526 geehlkeiekeaeeivdevl 545 +e+hl+++ +ea+ +vde++ lcl|FitnessBrowser__Putida:PP_3578 525 DEAHLQRLVEEAQVLVDEAI 544 *****************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (545 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: 8.33 // [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