Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 8499455 DvMF_0227 phosphoglucomutase (RefSeq)
Query= CharProtDB::CH_002452 (546 letters) >FitnessBrowser__Miya:8499455 Length = 549 Score = 686 bits (1771), Expect = 0.0 Identities = 341/547 (62%), Positives = 416/547 (76%), Gaps = 1/547 (0%) Query: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60 MA H +AGQ + S L+++ L A YY P+ E V FGTSGHRG A SFNE H Sbjct: 1 MATHPQAGQRPEASQLVDIPALVAAYYTEHPDTAAPERRVSFGTSGHRGGALSGSFNEEH 60 Query: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 ILA+ QA+ E RA+ GITGP ++G DTHALSEPA + LEVLAANGV ++Q+ G+TPT Sbjct: 61 ILAVTQAVCEYRAQAGITGPLFLGMDTHALSEPAHRTALEVLAANGVSTVIQQGGGYTPT 120 Query: 121 PAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179 P +S+AIL N + L DGIVITPSHNPPEDGG KYNPP+GGPADT+ TK ++ RAN Sbjct: 121 PVISHAILTWNAGRAQGLGDGIVITPSHNPPEDGGFKYNPPHGGPADTDATKWIQRRANE 180 Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239 LL DG + V+R+ L +A+A+ V ++D V+ +V LA +VDM AI+ AGL LG DPLGGS Sbjct: 181 LLDDGNRAVRRMHLRDALAAPCVSQRDFVRGYVADLASVVDMPAIKAAGLKLGADPLGGS 240 Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299 + YW I E Y L++T+VND VD TFRFM LDKDG IRMDCSS AMAGL+ LRDKFD+ Sbjct: 241 SLAYWHPIAEAYGLDITVVNDAVDPTFRFMPLDKDGKIRMDCSSPWAMAGLINLRDKFDV 300 Query: 300 AFANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVV 359 AF ND D DRHGIVT +GLMNPNHYLAVA+ YLF+HRPQW AVGKTLV+S+M+DRV Sbjct: 301 AFGNDADADRHGIVTASGLMNPNHYLAVAVWYLFRHRPQWSPQCAVGKTLVTSSMVDRVA 360 Query: 360 NDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAA 419 LGRK+VEVPVGFKWFV L +GS GFGGEESAGASFLR DGT W+TDKDG+++ LLAA Sbjct: 361 ASLGRKVVEVPVGFKWFVQPLLEGSCGFGGEESAGASFLRRDGTVWTTDKDGLLLNLLAA 420 Query: 420 EITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPIT 479 EI AV G++P E Y +L ++FGAP Y RLQ+ A + ++A L+ LSP++++A+ LAG PIT Sbjct: 421 EIMAVEGRDPAELYTKLTEQFGAPLYERLQSPAGAERRAVLANLSPDVLTATELAGAPIT 480 Query: 480 ARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIV 539 A LT APGN ASIGGLKV+TD+GWFAARPSGTED YKIY ESF G +H K+I++EAV+IV Sbjct: 481 AMLTKAPGNDASIGGLKVITDDGWFAARPSGTEDMYKIYTESFKGSDHLKRIQQEAVDIV 540 Query: 540 SEVLKNA 546 A Sbjct: 541 DRAFAAA 547 Lambda K H 0.316 0.134 0.395 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: 899 Number of extensions: 42 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: 546 Length of database: 549 Length adjustment: 36 Effective length of query: 510 Effective length of database: 513 Effective search space: 261630 Effective search space used: 261630 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: 53 (25.0 bits)
Align candidate 8499455 DvMF_0227 (phosphoglucomutase (RefSeq))
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.3521.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-282 923.4 0.0 2.1e-282 923.3 0.0 1.0 1 lcl|FitnessBrowser__Miya:8499455 DvMF_0227 phosphoglucomutase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499455 DvMF_0227 phosphoglucomutase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 923.3 0.0 2.1e-282 2.1e-282 1 545 [. 1 544 [. 1 545 [. 1.00 Alignments for each domain: == domain 1 score: 923.3 bits; conditional E-value: 2.1e-282 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGi 77 ma +p+aGq++++++l+d+++lva+yy+ +pd+ ++++v+fGtsGhrG al g+fne+hila++qav e+ra+ Gi lcl|FitnessBrowser__Miya:8499455 1 MATHPQAGQRPEASQLVDIPALVAAYYTEHPDTAAPERRVSFGTSGHRGGALSGSFNEEHILAVTQAVCEYRAQAGI 77 789************************************************************************** PP TIGR01132 78 tGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnppedG 154 tGpl++G+dthalsepa+ ++levlaan+v++++q+ +ytptp +shailt+n g+ ++l dGivitpshnppedG lcl|FitnessBrowser__Miya:8499455 78 TGPLFLGMDTHALSEPAHRTALEVLAANGVSTVIQQGGGYTPTPVISHAILTWNAGRAQGLGDGIVITPSHNPPEDG 154 ***************************************************************************** PP TIGR01132 155 GikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglr 231 G+kynpp+GGpa+t++tk+i+ ranell d++++v+r++l al++ v ++d+v+ yv+dla vvd+ ai+ agl+ lcl|FitnessBrowser__Miya:8499455 155 GFKYNPPHGGPADTDATKWIQRRANELLDDGNRAVRRMHLRDALAAPCVSQRDFVRGYVADLASVVDMPAIKAAGLK 231 ***************************************************************************** PP TIGR01132 232 lGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndada 308 lG+dplGG+++ yw++iae+y+ld+t+vn+avd+tfrfm ldkdGkirmdcssp amagl++l+dk+d+afgndada lcl|FitnessBrowser__Miya:8499455 232 LGADPLGGSSLAYWHPIAEAYGLDITVVNDAVDPTFRFMPLDKDGKIRMDCSSPWAMAGLINLRDKFDVAFGNDADA 308 ***************************************************************************** PP TIGR01132 309 drhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldg 385 drhGivt +Gl+npnhylava++yl++hr+qw+ + avGktlv+s+++drv+a+lgrk+vevpvGfkwfv+ ll+g lcl|FitnessBrowser__Miya:8499455 309 DRHGIVTA-SGLMNPNHYLAVAVWYLFRHRPQWSPQCAVGKTLVTSSMVDRVAASLGRKVVEVPVGFKWFVQPLLEG 384 *******9.9******************************************************************* PP TIGR01132 386 slGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarl 462 s GfGGeesaGasflr+dGtvw+tdkdG++l+llaaei+av G++p + y +l++++G+p+y+r++++a ++++a+l lcl|FitnessBrowser__Miya:8499455 385 SCGFGGEESAGASFLRRDGTVWTTDKDGLLLNLLAAEIMAVEGRDPAELYTKLTEQFGAPLYERLQSPAGAERRAVL 461 ***************************************************************************** PP TIGR01132 463 kklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaee 539 ++lspd ++at+laG +ita ltkapGn+a+iGGlkv+td+gwfaarpsGted+ykiy+esfkg++hlk+i++ea + lcl|FitnessBrowser__Miya:8499455 462 ANLSPDVLTATELAGAPITAMLTKAPGNDASIGGLKVITDDGWFAARPSGTEDMYKIYTESFKGSDHLKRIQQEAVD 538 ***************************************************************************** PP TIGR01132 540 ivdevl 545 ivd+++ lcl|FitnessBrowser__Miya:8499455 539 IVDRAF 544 ***986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (549 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 7.59 // [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