GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas fluorescens GW456-L13

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.11333.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: 9.99
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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