Alignments for a candidate for gnd in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Sinorhizobium meliloti 1021

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate SMc04262 SMc04262 6-phosphogluconate dehydrogenase

Query= BRENDA::P12013
         (468 letters)



>FitnessBrowser__Smeli:SMc04262
          Length = 476

 Score =  451 bits (1161), Expect = e-131
 Identities = 222/465 (47%), Positives = 312/465 (67%), Gaps = 3/465 (0%)

Query: 5   IGVIGLGVMGSNIALNMANKGENVAVYNYTRDLTDQLIQKLDG--QSLSPYYELEDFVQS 62
           IG+IGLGVMGSN+ALN+A KG  +AV+N T D T +   +       + P   +E+FV +
Sbjct: 6   IGLIGLGVMGSNLALNIAEKGNRIAVFNRTVDATRKFYAEAGALKDQIVPCETIEEFVAA 65

Query: 63  LEKPRKIFLMVTAGKPVDSVIQSLKPLLEEGDVIMDGGNSHYEDTERRYDELKEKGIGYL 122
           +  PR I +M+ AG PVD  +++LKP L +GD+++D GN+++ DT RR+D LK+ G+ ++
Sbjct: 66  IRPPRPIIIMIKAGDPVDQQMEALKPHLAKGDIMIDAGNANFRDTMRRFDALKDSGLTFI 125

Query: 123 GVGISGGEVGALTGPSIMPGGDRDVYEKAAPILTKIAAQVGDDPCCVYIGPKGAGHFTKM 182
           G+G+SGGE GA  GPSIM GG  + Y +   +LT IAA+   DPC  ++G  GAGHF K 
Sbjct: 126 GMGVSGGEEGARHGPSIMVGGTEESYRRVEKVLTSIAAKYDSDPCVAWLGENGAGHFVKT 185

Query: 183 VHNGIEYADMQLIAEAYTFLRETLRLPLDEIASIFETWNQGELKSYLIEITAEILRKKDE 242
           +HNGIEYADMQ+IAE Y  LR+ L++   EI  +F  WN+G L SYLIEIT ++L+  D 
Sbjct: 186 IHNGIEYADMQMIAEIYGILRDGLKMTAQEIGEVFGAWNKGRLNSYLIEITEKVLKAADP 245

Query: 243 KTGQPLIDVILDKTGQKGTGKWTSMQAIDNGIPSTIITESLFARYLSSLKEERMAAQDVL 302
            TG+P++D+ILDK GQKGTGKW+ ++A + G+P+T I  ++ AR +SS KEER AA+ VL
Sbjct: 246 LTGKPIVDMILDKAGQKGTGKWSVIEAQNMGVPATAIEAAVAARSISSAKEEREAAEKVL 305

Query: 303 A-GPEAEEKHLDKDTWIEYVRQALYMGKVCAYAQGFAQYKMSSELYGWNLPLKDIALIFR 361
              P  E K  D+D +I+ +  AL   K+ AYAQGFA    +S+ +GWNLP+  IA I+R
Sbjct: 306 GLPPVGEIKVADRDGFIKDLENALLAAKIGAYAQGFAVMAAASKEFGWNLPMPTIAKIWR 365

Query: 362 GGCIIRADFLNVISEAFSEQPNLANLLIAPYFTDKLHAYQTGLRKVVCEGISTGISFPCL 421
            GCIIR+ FL+ I+ AF++ P+ ANL++ P F   +      LR+VV   +  G+  P L
Sbjct: 366 AGCIIRSQFLDEITTAFTKAPDAANLIVTPAFAAMVKESDGALRRVVSTAVLGGLPVPAL 425

Query: 422 TTALSYYDGYRTGRSNANLLQAQRDYFGAHTYERTDMDGVFHTNW 466
            +AL Y+D YR GR  AN++QAQRD+FGAH ++R D     H  W
Sbjct: 426 ASALGYFDSYRRGRGTANVIQAQRDFFGAHGFDRVDGADSHHGPW 470


Lambda     K      H
   0.318    0.137    0.403 

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: 540
Number of extensions: 17
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: 468
Length of database: 476
Length adjustment: 33
Effective length of query: 435
Effective length of database: 443
Effective search space:   192705
Effective search space used:   192705
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: 51 (24.3 bits)

Align candidate SMc04262 SMc04262 (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.26031.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.9e-194  632.7   0.0   2.2e-194  632.5   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04262  SMc04262 6-phosphogluconate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04262  SMc04262 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.5   0.0  2.2e-194  2.2e-194       1     465 [.       5     470 ..       5     472 .. 0.97

  Alignments for each domain:
  == domain 1  score: 632.5 bits;  conditional E-value: 2.2e-194
                           TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeak.gkklvgaesieefvkslekPrkilllvkaG 74 
                                         +iGliGl+vmG+nl+lnia+kG  +av+nrt + t+++ +e+   + ++v+ e+ieefv++++ Pr i++++kaG
  lcl|FitnessBrowser__Smeli:SMc04262   5 EIGLIGLGVMGSNLALNIAEKGNRIAVFNRTVDATRKFYAEAGAlKDQIVPCETIEEFVAAIRPPRPIIIMIKAG 79 
                                         69*************************************998652678*************************** PP

                           TIGR00873  75 aavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayelv 149
                                         ++vd+ +e+l+p+l kgdi+id Gn++++dt+rr ++lk+ g++f+G+GvsGGeeGar+GPs+m GG++e+y+ v
  lcl|FitnessBrowser__Smeli:SMc04262  80 DPVDQQMEALKPHLAKGDIMIDAGNANFRDTMRRFDALKDSGLTFIGMGVSGGEEGARHGPSIMVGGTEESYRRV 154
                                         *************************************************************************** PP

                           TIGR00873 150 epilqkiaakvegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnegeld 224
                                         e +l++iaak + +pc+ ++Ge+GaGh+vk +hnGiey+dmq+iae y +l+++lk++a+ei evf  Wn+g+l+
  lcl|FitnessBrowser__Smeli:SMc04262 155 EKVLTSIAAKYDSDPCVAWLGENGAGHFVKTIHNGIEYADMQMIAEIYGILRDGLKMTAQEIGEVFGAWNKGRLN 229
                                         *************************************************************************** PP

                           TIGR00873 225 sylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaaskl 298
                                         sylieit+++lk+ d   Gkp+vd+ild+agqkGtGkW++i+a ++GvP t i ++v ar +ss keer aa+k+
  lcl|FitnessBrowser__Smeli:SMc04262 230 SYLIEITEKVLKAADPLtGKPIVDMILDKAGQKGTGKWSVIEAQNMGVPATAIEAAVAARSISSAKEEREAAEKV 304
                                         ***************977********************************************************* PP

                           TIGR00873 299 lsg.plaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkik 372
                                         l   p+ e k  d++ fi+d+++al+a+ki +yaqGfa++++aske+gw+l +++ia+iwr+Gciirs+fld+i+
  lcl|FitnessBrowser__Smeli:SMc04262 305 LGLpPVGEIKVADRDGFIKDLENALLAAKIGAYAQGFAVMAAASKEFGWNLPMPTIAKIWRAGCIIRSQFLDEIT 379
                                         **9566667777*************************************************************** PP

                           TIGR00873 373 kafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGa 447
                                         +af++ p+++nl++ + f+ ++k++  +lr+vv++a+  g+pvPal++al ++d+yr+ r +an++qaqrd+fGa
  lcl|FitnessBrowser__Smeli:SMc04262 380 TAFTKAPDAANLIVTPAFAAMVKESDGALRRVVSTAVLGGLPVPALASALGYFDSYRRGRGTANVIQAQRDFFGA 454
                                         *************************************************************************** PP

                           TIGR00873 448 htyertdkprgeffhteW 465
                                         h+++r d      +h  W
  lcl|FitnessBrowser__Smeli:SMc04262 455 HGFDRVDGAD--SHHGPW 470
                                         *****99654..566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (476 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: 7.50
//
[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