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.2561.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.24
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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