Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate 201480 SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file)
Query= BRENDA::A0A0H3NJ17 (546 letters) >FitnessBrowser__MR1:201480 Length = 550 Score = 645 bits (1665), Expect = 0.0 Identities = 321/548 (58%), Positives = 405/548 (73%), Gaps = 5/548 (0%) Query: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAGRHSFNEPH 60 MAIH RAGQ A Q DL+N+ +L + YY +KP AE V FGTSGHRG+A + SFN+ H Sbjct: 1 MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDH 60 Query: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 I AI QA+ + R I GP ++G DTHALS A++S +EVLAAN V V +Q+N+GFTPT Sbjct: 61 IWAITQAVVDYRQSVNIEGPLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPT 120 Query: 121 PAVSNAILVHN----KKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDR 176 P VS+AI+ N + G L+DG++ITPSHNPP+DGGIKYNPP+GGPA+ N+T +E R Sbjct: 121 PVVSHAIICANHAAAQNGALLSDGLIITPSHNPPQDGGIKYNPPHGGPAEGNITAWIESR 180 Query: 177 ANALLAGGLQGVKRISLDAAMASGHVKAVDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236 AN L L+GV +++ A+ASG+V A+DL+ P+V L ++VDM AI KA L LGVDPL Sbjct: 181 ANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGVDPL 240 Query: 237 GGSGIEYWKRIAEHYKLNLTLVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDK 296 GGSGI YW IA+HY +++TLVND+VD +F FM LDKDG IRMDCSS AMAGLLA ++ Sbjct: 241 GGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKES 300 Query: 297 FDLAFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPLWGKDVAVGKTLVSSAMI 355 FDL NDPDYDRHGIV P GLM+PNHYLAVAI+YL HRP W +A+GKTLVSSA+I Sbjct: 301 FDLCVGNDPDYDRHGIVCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALI 360 Query: 356 DRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMC 415 D++ G+KL+EVPVGFKWFVDGL + + FGGEESAGA+FLR DGT W TDKDG I+ Sbjct: 361 DKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGEESAGAAFLRRDGTTWCTDKDGFILV 420 Query: 416 LLAAEITAVTGKNPQEHYNELAARFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAG 475 LLAAE+ AVTGK P + + EL A+FG Y R+ + + KA +KL+ + ++A+ LAG Sbjct: 421 LLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLNATMLAG 480 Query: 476 DPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEA 535 + I A LT APGN ASIGG+KV T NGWFAARPSGTE +KIY ESF+ E+H +I K+A Sbjct: 481 EKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDA 540 Query: 536 VEIVSEVL 543 ++ + L Sbjct: 541 QALIDKAL 548 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: 885 Number of extensions: 35 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: 546 Length of database: 550 Length adjustment: 36 Effective length of query: 510 Effective length of database: 514 Effective search space: 262140 Effective search space used: 262140 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 201480 SO2336 (phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file))
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.4896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-261 853.0 0.9 4.8e-261 852.8 0.9 1.0 1 lcl|FitnessBrowser__MR1:201480 SO2336 phosphoglucomutase, alpha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201480 SO2336 phosphoglucomutase, alpha-D-glucose phosphate-specific (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 852.8 0.9 4.8e-261 4.8e-261 1 545 [. 1 548 [. 1 549 [. 0.99 Alignments for each domain: == domain 1 score: 852.8 bits; conditional E-value: 4.8e-261 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 mai++raGq a q dl++++kl+++yy++kp+ + a+q+v+fGtsGhrG+a +g+fn+ hi ai+qavv++r+ i G lcl|FitnessBrowser__MR1:201480 1 MAIHQRAGQIASQMDLVNIPKLMSHYYSIKPNMDAAEQRVTFGTSGHRGTAFQGSFNQDHIWAITQAVVDYRQSVNIEG 79 89***************************************************************************** PP TIGR01132 80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkea...ladGivitpshnppedGG 155 pl++G dthals a+vs++evlaan+v v +q+n+++tptp vshai+ n++ ++ l+dG++itpshnpp+dGG lcl|FitnessBrowser__MR1:201480 80 PLFLGIDTHALSYAAYVSAIEVLAANKVTVYIQQNDGFTPTPVVSHAIICANHAAAQNgalLSDGLIITPSHNPPQDGG 158 **************************************************9986544322378**************** PP TIGR01132 156 ikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGv 234 ikynpp+GGpae+++t +ie ran++l++ lkgv +l ++ al+s+ v++ dl++pyv+dl +vvd+ ai ka+l+lGv lcl|FitnessBrowser__MR1:201480 159 IKYNPPHGGPAEGNITAWIESRANDYLRAALKGVNKLAYADALASGYVHAIDLITPYVADLENVVDMHAIAKANLKLGV 237 ******************************************************************************* PP TIGR01132 235 dplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGi 313 dplGG+g++yw +ia++y++d+tlvn++vd++f fm+ldkdGkirmdcsspyamagll+ k+ +dl +gnd+d+drhGi lcl|FitnessBrowser__MR1:201480 238 DPLGGSGIHYWAPIAKHYGIDITLVNDKVDPSFSFMSLDKDGKIRMDCSSPYAMAGLLAHKESFDLCVGNDPDYDRHGI 316 ******************************************************************************* PP TIGR01132 314 vtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGe 392 v p +Gl++pnhylavai+yl +hr++w++++a+Gktlvssalid++ g+kl+evpvGfkwfvdGl ++++ fGGe lcl|FitnessBrowser__MR1:201480 317 VCPGTGLMDPNHYLAVAIDYLLTHRPEWSDSLAIGKTLVSSALIDKICVFHGKKLLEVPVGFKWFVDGLAEATIAFGGE 395 ******************************************************************************* PP TIGR01132 393 esaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevs 471 esaGa+flr+dGt+w+tdkdG il llaae++avtGk+p+qr++el a++G+ +y+rid++ + ++ka+++kl +d++ lcl|FitnessBrowser__MR1:201480 396 ESAGAAFLRRDGTTWCTDKDGFILVLLAAEMLAVTGKTPGQRHQELVAQFGQSFYKRIDSPISLENKAKFAKLNADTLN 474 ******************************************************************************* PP TIGR01132 472 attlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545 at laG+ i a lt+apGn+a+iGG+kvtt +gwfaarpsGte ++kiy esf e+hl ei k+a++++d++l lcl|FitnessBrowser__MR1:201480 475 ATMLAGEKIEAVLTHAPGNNASIGGIKVTTTNGWFAARPSGTEALFKIYGESFISEQHLAEIIKDAQALIDKAL 548 **********************************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (550 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.32 // [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