Alignments for a candidate for gnd in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Synechococcus elongatus PCC 7942

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate Synpcc7942_0039 Synpcc7942_0039 6-phosphogluconate dehydrogenase

Query= BRENDA::P80859
         (469 letters)



>FitnessBrowser__SynE:Synpcc7942_0039
          Length = 471

 Score =  567 bits (1461), Expect = e-166
 Identities = 282/470 (60%), Positives = 367/470 (78%), Gaps = 3/470 (0%)

Query: 1   MSKQQIGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFLQE-AKGKNVVGTYSIEE 59
           M+ QQ G+IGLAVMG+NLALNIE  GFS++VYNR++ KTE F+ + A+GKN+V  YS+E+
Sbjct: 1   MALQQFGLIGLAVMGENLALNIERNGFSLTVYNRTAEKTEAFMADRAQGKNIVPAYSLED 60

Query: 60  FVQSLETPRKILLMVKAGTATDATIQSLLPHLEKDDILIDGGNTYYKDTQRRNKELAESG 119
           FV SLE PR+IL+MVKAG   DA ++ L P L+  D++IDGGN+ + DT+RR K+L   G
Sbjct: 61  FVASLERPRRILVMVKAGGPVDAVVEQLKPLLDPGDLIIDGGNSLFTDTERRVKDLEALG 120

Query: 120 IHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKVDGEPCTTYIGPDGAGH 179
           + F+G GVSGGEEGAL GPS+MPGG + A+E V+PI+ +I+A+VD  PC TYIGP G+GH
Sbjct: 121 LGFMGMGVSGGEEGALNGPSLMPGGTQAAYEAVEPIVRSIAAQVDDGPCVTYIGPGGSGH 180

Query: 180 YVKMVHNGIEYGDMQLISESYFILKQVLGLSADELHEVFAEWNKG-ELDSYLIEITADIF 238
           YVKMVHNGIEYGDMQLI+E+Y +LK V GL+A ELH+VFA WNK  ELDS+LIEITADIF
Sbjct: 181 YVKMVHNGIEYGDMQLIAEAYDLLKSVAGLNASELHDVFAAWNKTPELDSFLIEITADIF 240

Query: 239 TKKDE-ETGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPIITESVFARFISAMKEERV 297
           TK D+  TG+PLV++ILD AGQKGTG+WT ++AL++GV +P I  +V AR +S++K ER 
Sbjct: 241 TKVDDLGTGQPLVELILDAAGQKGTGRWTVETALEIGVAIPTIIAAVNARILSSIKAERQ 300

Query: 298 KASGLLSGPEVKPVTENKEELIEAVRKALFMSKICSYAQGFAQMKAASEEYNWDLKYGEI 357
            AS +LSGP  +P + +++  I++VR AL+ SKICSYAQG A +  AS+ YN+ L  GE+
Sbjct: 301 AASEILSGPITEPFSGDRQAFIDSVRDALYCSKICSYAQGMALLAKASQVYNYGLNLGEL 360

Query: 358 AMIFRGGCIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVESYQGALRQVISLAVAQGV 417
           A I++GGCIIRA FL KIK+AYD +P L NLLL   F+  +   Q A R+VI++A  +G+
Sbjct: 361 ARIWKGGCIIRAGFLNKIKQAYDADPTLANLLLAPEFRQTILDRQLAWRRVIAIAAERGI 420

Query: 418 PVPSFSSALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDKEGIFHTEW 467
           PVP+FS++L Y+DSYR   LP NL QAQRDYFGAHTYERTD+ G FH +W
Sbjct: 421 PVPAFSASLDYFDSYRRDRLPQNLTQAQRDYFGAHTYERTDRSGSFHAQW 470


Lambda     K      H
   0.315    0.134    0.379 

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: 604
Number of extensions: 22
Number of successful extensions: 5
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: 469
Length of database: 471
Length adjustment: 33
Effective length of query: 436
Effective length of database: 438
Effective search space:   190968
Effective search space used:   190968
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 (21.5 bits)
S2: 51 (24.3 bits)

Align candidate Synpcc7942_0039 Synpcc7942_0039 (6-phosphogluconate dehydrogenase)
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))

# 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/TIGR00873.hmm
# target sequence database:        /tmp/gapView.12944.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00873  [M=467]
Accession:   TIGR00873
Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.3e-220  717.2   0.0   4.9e-220  717.1   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_0039  Synpcc7942_0039 6-phosphoglucona


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_0039  Synpcc7942_0039 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.1   0.0  4.9e-220  4.9e-220       1     465 [.       5     470 ..       5     471 .] 0.99

  Alignments for each domain:
  == domain 1  score: 717.1 bits;  conditional E-value: 4.9e-220
                                 TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkill 69 
                                               ++GliGlavmG+nl+lni+++Gfs++vynrt ekt+++++++a+gk++v+a+s+e+fv+sle+Pr+il+
  lcl|FitnessBrowser__SynE:Synpcc7942_0039   5 QFGLIGLAVMGENLALNIERNGFSLTVYNRTAEKTEAFMADRAQGKNIVPAYSLEDFVASLERPRRILV 73 
                                               68******************************************************************* PP

                                 TIGR00873  70 lvkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslm 138
                                               +vkaG +vdav+e+l+pll++gd+iidGGnsl++dterr+k+l++ g+ f+G+GvsGGeeGa++GPslm
  lcl|FitnessBrowser__SynE:Synpcc7942_0039  74 MVKAGGPVDAVVEQLKPLLDPGDLIIDGGNSLFTDTERRVKDLEALGLGFMGMGVSGGEEGALNGPSLM 142
                                               ********************************************************************* PP

                                 TIGR00873 139 pGGskeayelvepilqkiaakvegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealkls 207
                                               pGG+++aye+vepi+++iaa+v++ pc++yiG++G+GhyvkmvhnGieygdmqliaeay+llk++ +l+
  lcl|FitnessBrowser__SynE:Synpcc7942_0039 143 PGGTQAAYEAVEPIVRSIAAQVDDGPCVTYIGPGGSGHYVKMVHNGIEYGDMQLIAEAYDLLKSVAGLN 211
                                               ********************************************************************* PP

                                 TIGR00873 208 aeeiaevfeeWne.geldsylieitadilkkkded..GkplvdkildaagqkGtGkWtaidaldlGvPv 273
                                               a+e+++vf+ Wn+  elds+lieitadi++k d+   G+plv+ ildaagqkGtG+Wt++ al+ Gv +
  lcl|FitnessBrowser__SynE:Synpcc7942_0039 212 ASELHDVFAAWNKtPELDSFLIEITADIFTKVDDLgtGQPLVELILDAAGQKGTGRWTVETALEIGVAI 280
                                               ************9469*************998875469******************************* PP

                                 TIGR00873 274 tlitesvfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeask 342
                                                +i+++v ar+lss+k er aas+ lsgp +e  + d+++fi++vr+aly+ski+syaqG+all++as+
  lcl|FitnessBrowser__SynE:Synpcc7942_0039 281 PTIIAAVNARILSSIKAERQAASEILSGPITEPFSGDRQAFIDSVRDALYCSKICSYAQGMALLAKASQ 349
                                               *********************************999********************************* PP

                                 TIGR00873 343 eygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaiel 411
                                                y++ lnlge+a+iw+gGciir+ fl+kik+a++++p l+nllla+ f++++ ++q ++r+v+a a+e 
  lcl|FitnessBrowser__SynE:Synpcc7942_0039 350 VYNYGLNLGELARIWKGGCIIRAGFLNKIKQAYDADPTLANLLLAPEFRQTILDRQLAWRRVIAIAAER 418
                                               ********************************************************************* PP

                                 TIGR00873 412 gipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteW 465
                                               gipvPa+sa+l+++d+yr++rlp+nl+qaqrdyfGahtyertd+ +   fh++W
  lcl|FitnessBrowser__SynE:Synpcc7942_0039 419 GIPVPAFSASLDYFDSYRRDRLPQNLTQAQRDYFGAHTYERTDRSG--SFHAQW 470
                                               *******************************************999..9***** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (471 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.53
//
[ok]

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

Downloads

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

Related tools

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