Alignments for a candidate for pgmA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmA in Pseudomonas putida KT2440

Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate PP_3578 PP_3578 phosphoglucomutase

Query= BRENDA::I6Y2G3
         (547 letters)



>FitnessBrowser__Putida:PP_3578
          Length = 545

 Score =  647 bits (1670), Expect = 0.0
 Identities = 341/549 (62%), Positives = 400/549 (72%), Gaps = 8/549 (1%)

Query: 1   MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60
           M  +P AG+PA    LVD+P L+TAYY+  PD    AQ+VAFGTSGHRGS+L  +FNE H
Sbjct: 1   MTLSPLAGKPAPASVLVDIPRLLTAYYTGRPDATVAAQRVAFGTSGHRGSSLELSFNEYH 60

Query: 61  ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120
           +LAI+QAI  YR  +G  GPLFIG DTH LS PA  SALEVLAAN V  ++   D YTPT
Sbjct: 61  VLAISQAICLYRQEKGIDGPLFIGADTHALSAPATASALEVLAANGVQVMLSKDDEYTPT 120

Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180
           PA+SHAIL +NRGRT+ LADGIV+TPSHNPP  GG KYNPPNGGPAD+  T  I  +ANE
Sbjct: 121 PAVSHAILCHNRGRTQGLADGIVITPSHNPPQSGGFKYNPPNGGPADSDVTKWIEGKANE 180

Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237
           +L A  + VKR+  A+AL+  T  RHDY+ +YV DL NV+D   IR AG+R+G DPLGGA
Sbjct: 181 LLAANLAGVKRMDHAQALQAPTTHRHDYVSNYVADLENVIDFDVIRGAGLRLGVDPLGGA 240

Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297
            V YW  IA  + LDL VVN  VD T+RFMT+D DG+IRMD SSP AM GLI    G RE
Sbjct: 241 GVRYWSAIAKHYQLDLEVVNTEVDPTFRFMTVDWDGQIRMDPSSPYAMQGLI----GLRE 296

Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357
           R+ +A   D D DRHGIVTPD GLL PN+YLAVAI+YL+ HRP W +  AVGKTVVSS +
Sbjct: 297 RFDVAFACDPDHDRHGIVTPD-GLLQPNNYLAVAIDYLFRHRPQWRSDAAVGKTVVSSGL 355

Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417
           IDRV   +GR L EVPVGFK+F  GL   +LGFGGEESAGASFLRRDGSVW TDKDG+I 
Sbjct: 356 IDRVTQRLGRDLYEVPVGFKFFAQGLFDGSLGFGGEESAGASFLRRDGSVWATDKDGLIP 415

Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477
           ALLAAE+ A TG  PSQ Y  L    G P   R++A AD  QKA L++L+ +QV +TELA
Sbjct: 416 ALLAAEMTARTGRNPSQAYADLTEALGKPFATRVEAKADARQKALLSKLAPEQVKSTELA 475

Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537
           GEPI   L+ APGNG A+GGLKV TAN WFAARPSGTED+YKIYAESF    HL  + + 
Sbjct: 476 GEPIVQILSHAPGNGQAIGGLKVMTANGWFAARPSGTEDIYKIYAESFIDEAHLQRLVEE 535

Query: 538 AREVVDRVI 546
           A+ +VD  I
Sbjct: 536 AQVLVDEAI 544


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: 961
Number of extensions: 31
Number of successful extensions: 4
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: 545
Length adjustment: 35
Effective length of query: 512
Effective length of database: 510
Effective search space:   261120
Effective search space used:   261120
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: 52 (24.6 bits)

Align candidate PP_3578 PP_3578 (phosphoglucomutase)
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.6546.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.9e-269  880.5   0.0   2.1e-269  880.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3578  PP_3578 phosphoglucomutase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3578  PP_3578 phosphoglucomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.4   0.0  2.1e-269  2.1e-269       1     545 [.       1     544 [.       1     545 [] 1.00

  Alignments for each domain:
  == domain 1  score: 880.4 bits;  conditional E-value: 2.1e-269
                           TIGR01132   1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 
                                         m++ p+aG++a+++ l+d+++l+++yy+ +pda  aaq+v+fGtsGhrGs+l+ +fne h+lai+qa+  +r+++
  lcl|FitnessBrowser__Putida:PP_3578   1 MTLSPLAGKPAPASVLVDIPRLLTAYYTGRPDATVAAQRVAFGTSGHRGSSLELSFNEYHVLAISQAICLYRQEK 75 
                                         6789*********************************************************************** PP

                           TIGR01132  76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnp 150
                                         Gi Gpl+iG dthals pa  s+levlaan+v+v++++ + ytptpavshail +n+g++++ladGivitpshnp
  lcl|FitnessBrowser__Putida:PP_3578  76 GIDGPLFIGADTHALSAPATASALEVLAANGVQVMLSKDDEYTPTPAVSHAILCHNRGRTQGLADGIVITPSHNP 150
                                         *************************************************************************** PP

                           TIGR01132 151 pedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaai 225
                                         p+ GG+kynppnGGpa+++vtk+ie +anell+++l+gvkr+d ++al++ t++++d+v++yv+dl +v+d+++i
  lcl|FitnessBrowser__Putida:PP_3578 151 PQSGGFKYNPPNGGPADSDVTKWIEGKANELLAANLAGVKRMDHAQALQAPTTHRHDYVSNYVADLENVIDFDVI 225
                                         *************************************************************************** PP

                           TIGR01132 226 rkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydl 300
                                         r aglrlGvdplGGagv yw  ia++y+ldl +vn +vd+tfrfmt+d+dG+irmd sspyam gl+ l++++d+
  lcl|FitnessBrowser__Putida:PP_3578 226 RGAGLRLGVDPLGGAGVRYWSAIAKHYQLDLEVVNTEVDPTFRFMTVDWDGQIRMDPSSPYAMQGLIGLRERFDV 300
                                         *************************************************************************** PP

                           TIGR01132 301 afgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGf 375
                                         af+ d+d drhGivtp  Gll+pn ylavai+yl++hr+qw ++ avGkt+vss lidrv++ lgr+l+evpvGf
  lcl|FitnessBrowser__Putida:PP_3578 301 AFACDPDHDRHGIVTP-DGLLQPNNYLAVAIDYLFRHRPQWRSDAAVGKTVVSSGLIDRVTQRLGRDLYEVPVGF 374
                                         ****************.9********************************************************* PP

                           TIGR01132 376 kwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyari 450
                                         k+f +Gl+dgslGfGGeesaGasflr+dG+vw+tdkdG+i allaae+ta tG+np+q y +l++ +G+p+ +r+
  lcl|FitnessBrowser__Putida:PP_3578 375 KFFAQGLFDGSLGFGGEESAGASFLRRDGSVWATDKDGLIPALLAAEMTARTGRNPSQAYADLTEALGKPFATRV 449
                                         *************************************************************************** PP

                           TIGR01132 451 daaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfk 525
                                         +a a++ qka l+kl+p++v +t+laG++i   l++apGng aiGGlkv+t++gwfaarpsGted+ykiyaesf 
  lcl|FitnessBrowser__Putida:PP_3578 450 EAKADARQKALLSKLAPEQVKSTELAGEPIVQILSHAPGNGQAIGGLKVMTANGWFAARPSGTEDIYKIYAESFI 524
                                         *************************************************************************** PP

                           TIGR01132 526 geehlkeiekeaeeivdevl 545
                                         +e+hl+++ +ea+ +vde++
  lcl|FitnessBrowser__Putida:PP_3578 525 DEAHLQRLVEEAQVLVDEAI 544
                                         *****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (546 nodes)
Target sequences:                          1  (545 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: 10.70
//
[ok]

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

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Protein sequences (fasta format)
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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