Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas fluorescens FW300-N1B4

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate Pf1N1B4_4886 Phosphoglucomutase (EC 5.4.2.2)

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886
          Length = 548

 Score =  652 bits (1682), Expect = 0.0
 Identities = 344/549 (62%), Positives = 402/549 (73%), Gaps = 7/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA  E LVD+P LVTAYY+ +PD     Q+VAFGTSGHRGS+   +FNE H
Sbjct: 1   MTLSPFAGKPAPAELLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLSFNEWH 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 PAISHAILCYNRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANE 180

Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L A+ + VKR+   +AL+  T  RHDYL  YV DL NV+D  AIREA +R+G DPLGGA
Sbjct: 181 LLAAKLAGVKRISYEQALKASTTHRHDYLNTYVADLINVIDFDAIREAKLRLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA  + LDL VVN  VDAT+RFMT+D DG+IRMD SS  AM GLI    G +E
Sbjct: 241 GVRYWSAIAEHYRLDLEVVNKQVDATFRFMTVDWDGQIRMDPSSSHAMQGLI----GLKE 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ +A   D D DRHGIVTP  GLL PN+YLAV+I+YL+ +RP W A  AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPLWRADAAVGKTVVSSGL 356

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV   +GR+L EVPVGFKWF DGL   +LGFGGEESAGASFLR+DGSVW TDKDG+I 
Sbjct: 357 IDRVAKRLGRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGSVWCTDKDGLIP 416

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ A TG  PSQ Y AL  E G P   R+DA A+ EQKA L++LS DQV++T+LA
Sbjct: 417 ALLAAEMTARTGRDPSQAYRALTDELGEPFSVRVDAKANPEQKALLSKLSPDQVTSTQLA 476

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GE I + L+ APGN  A+GGLKV T N WFAARPSGTED+YKIYAESF    HL ++   
Sbjct: 477 GEAIQSILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFVSDDHLKQLVAE 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: 966
Number of extensions: 38
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 Pf1N1B4_4886 (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.22829.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   3.3e-268  876.4   0.0   3.7e-268  876.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886  Phosphoglucomutase (EC 5.4.2.2)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886  Phosphoglucomutase (EC 5.4.2.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.2   0.0  3.7e-268  3.7e-268       1     545 [.       1     545 [.       1     546 [. 0.99

  Alignments for each domain:
  == domain 1  score: 876.2 bits;  conditional E-value: 3.7e-268
                                      TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilai 64 
                                                    m++ p aG++a++e l+d+++lv++yy+ +pda  ++q+v+fGtsGhrGs+   +fne h+lai
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886   1 MTLSPFAGKPAPAELLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGSSFDLSFNEWHVLAI 64 
                                                    678899********************************************************** PP

                                      TIGR01132  65 aqavvevraaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshail 128
                                                    +qa+  +r+aqGi Gpl++G dthals pa  s+levlaan+v v++ e + ytptpa+shail
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886  65 SQAICLYREAQGIDGPLFVGIDTHALSTPAGASALEVLAANGVTVMIAEGDEYTPTPAISHAIL 128
                                                    **************************************************************** PP

                                      TIGR01132 129 tynkgkkealadGivitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrl 192
                                                     yn+g++++ladGivitpshnpp+ GG kynp nGGpa+t++tk+ie +anell+++l+gvkr+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 129 CYNRGRTSGLADGIVITPSHNPPQSGGYKYNPTNGGPADTHITKWIEAKANELLAAKLAGVKRI 192
                                                    **************************************************************** PP

                                      TIGR01132 193 dlekalksetvkekdlvkpyvddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldl 256
                                                    ++e+alk++t++++d+++ yv+dl +v+d++air+a+lrlGvdplGGagv yw  iae+y ldl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 193 SYEQALKASTTHRHDYLNTYVADLINVIDFDAIREAKLRLGVDPLGGAGVRYWSAIAEHYRLDL 256
                                                    **************************************************************** PP

                                      TIGR01132 257 tlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtpdkGl 320
                                                     +vn++vdatfrfmt+d+dG+irmd ss +am gl+ lk+++d+af+ d+d drhGivtp+ Gl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 257 EVVNKQVDATFRFMTVDWDGQIRMDPSSSHAMQGLIGLKERFDVAFACDPDHDRHGIVTPSGGL 320
                                                    **************************************************************** PP

                                      TIGR01132 321 lnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlld 384
                                                    l pn ylav+i+yl+++r+ w a+ avGkt+vss lidrv+  lgr+l+evpvGfkwf dGl+d
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 321 LAPNNYLAVSIDYLFQNRPLWRADAAVGKTVVSSGLIDRVAKRLGRRLYEVPVGFKWFADGLFD 384
                                                    **************************************************************** PP

                                      TIGR01132 385 gslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiya 448
                                                    gslGfGGeesaGasflrkdG+vw+tdkdG+i allaae+ta tG++p+q y +l+ ++G+p+  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 385 GSLGFGGEESAGASFLRKDGSVWCTDKDGLIPALLAAEMTARTGRDPSQAYRALTDELGEPFSV 448
                                                    **************************************************************** PP

                                      TIGR01132 449 ridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsG 512
                                                    r+da a+++qka l+klspd+v++t+laG+ai + l++apGn+ aiGGlkv+t++gwfaarpsG
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 449 RVDAKANPEQKALLSKLSPDQVTSTQLAGEAIQSILSHAPGNDQAIGGLKVMTENGWFAARPSG 512
                                                    **************************************************************** PP

                                      TIGR01132 513 tedvykiyaesfkgeehlkeiekeaeeivdevl 545
                                                    ted+ykiyaesf  ++hlk++  ea+ +vd ++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4886 513 TEDIYKIYAESFVSDDHLKQLVAEAQTLVDGAI 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: 11.29
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources