Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PfGW456L13_3066 Phosphoglucomutase (EC 5.4.2.2)
Query= BRENDA::I6Y2G3
(547 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066
Length = 548
Score = 644 bits (1661), Expect = 0.0
Identities = 339/549 (61%), Positives = 399/549 (72%), Gaps = 7/549 (1%)
Query: 1 MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
M +P AG+PA + LVD+P LVTAYY+ +PD Q+VAFGTSGHRGS+ +FNE H
Sbjct: 1 MTLSPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLSFNEWH 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 PAISHAILCYNRGRTTGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANE 180
Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
+L + + VKR+ +AL+ T RHDYL YV DL NV+D AIR+A +R+G DPLGGA
Sbjct: 181 LLANKLAGVKRISYEQALKASTTHRHDYLNTYVADLINVIDFDAIRDAKLRLGVDPLGGA 240
Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
V YW IA + LDL VVN VD T+RFMT+D DG+IRMD SS AM GLI G +E
Sbjct: 241 GVRYWSAIAEHYRLDLDVVNKEVDPTFRFMTVDWDGQIRMDPSSSHAMQGLI----GLKE 296
Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
R+ +A D D DRHGIVTP GLL PN+YLAVAI+YL+ +RP W A AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVAIDYLFQNRPQWRADAAVGKTVVSSGL 356
Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
IDRV + R+L EVPVGFKWF DGL +LGFGGEESAGASFLR+DG VW+TDKDG+I
Sbjct: 357 IDRVAKRLDRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGGVWSTDKDGLIP 416
Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
ALLAAE+ A TG PSQ Y AL E G P R+DA A+ EQKA L++LS QV++T+LA
Sbjct: 417 ALLAAEMTARTGRDPSQAYRALTDELGEPFSVRVDAKANPEQKALLSKLSPQQVTSTQLA 476
Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
GEPI + L+ APGN A+GGLKV T N WFAARPSGTED+YKIYAESF HL ++
Sbjct: 477 GEPIQSILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFVSDDHLKQLVAE 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: 982
Number of extensions: 40
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 PfGW456L13_3066 (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.23577.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.8e-268 876.6 0.0 3.2e-268 876.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 Phosphoglucomutase (EC 5.4.2.2)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 Phosphoglucomutase (EC 5.4.2.2)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 876.5 0.0 3.2e-268 3.2e-268 1 545 [. 1 545 [. 1 546 [. 0.99
Alignments for each domain:
== domain 1 score: 876.5 bits; conditional E-value: 3.2e-268
TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgt 55
m++ p aG++a+++ l+d+++lv++yy+ +pda ++q+v+fGtsGhrGs+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 1 MTLSPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLS 55
678899************************************************* PP
TIGR01132 56 fneahilaiaqavvevraaqGitGplyiGkdthalsepafvsvlevlaanqvevi 110
fne h+lai+qa+ +r+aqGi Gpl++G dthals pa s+levlaan+v v+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 56 FNEWHVLAISQAICLYREAQGIDGPLFVGIDTHALSTPAGASALEVLAANGVTVM 110
******************************************************* PP
TIGR01132 111 vqennrytptpavshailtynkgkkealadGivitpshnppedGGikynppnGGp 165
+ e + ytptpa+shail yn+g++ +ladGivitpshnpp+ GG kynp nGGp
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 111 IAEGDEYTPTPAISHAILCYNRGRTTGLADGIVITPSHNPPQSGGYKYNPTNGGP 165
******************************************************* PP
TIGR01132 166 aetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvv 220
a+t++tk+ie +anell+++l+gvkr+++e+alk++t++++d+++ yv+dl +v+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 166 ADTHITKWIEAKANELLANKLAGVKRISYEQALKASTTHRHDYLNTYVADLINVI 220
******************************************************* PP
TIGR01132 221 dlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkd 275
d++air+a+lrlGvdplGGagv yw iae+y ldl +vn++vd+tfrfmt+d+d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 221 DFDAIRDAKLRLGVDPLGGAGVRYWSAIAEHYRLDLDVVNKEVDPTFRFMTVDWD 275
******************************************************* PP
TIGR01132 276 GkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylava 330
G+irmd ss +am gl+ lk+++d+af+ d+d drhGivtp+ Gll pn ylava
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 276 GQIRMDPSSSHAMQGLIGLKERFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVA 330
******************************************************* PP
TIGR01132 331 ieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldg 385
i+yl+++r+qw a+ avGkt+vss lidrv+ l+r+l+evpvGfkwf dGl+dg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 331 IDYLFQNRPQWRADAAVGKTVVSSGLIDRVAKRLDRRLYEVPVGFKWFADGLFDG 385
******************************************************* PP
TIGR01132 386 slGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaa 440
slGfGGeesaGasflrkdG vwstdkdG+i allaae+ta tG++p+q y +l+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 386 SLGFGGEESAGASFLRKDGGVWSTDKDGLIPALLAAEMTARTGRDPSQAYRALTD 440
******************************************************* PP
TIGR01132 441 kyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiG 495
++G+p+ r+da a+++qka l+klsp++v++t+laG++i + l++apGn+ aiG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 441 ELGEPFSVRVDAKANPEQKALLSKLSPQQVTSTQLAGEPIQSILSHAPGNDQAIG 495
******************************************************* PP
TIGR01132 496 GlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevl 545
Glkv+t++gwfaarpsGted+ykiyaesf ++hlk++ ea+ +vd ++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3066 496 GLKVMTENGWFAARPSGTEDIYKIYAESFVSDDHLKQLVAEAQTLVDGAI 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.52
//
[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