Alignments for a candidate for gnd in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Echinicola vietnamensis KMM 6221, DSM 17526

Align 6-phosphogluconate dehydrogenase, decarboxylating; EC 1.1.1.44 (characterized)
to candidate Echvi_4222 Echvi_4222 6-phosphogluconate dehydrogenase, decarboxylating

Query= SwissProt::P70718
         (484 letters)



>FitnessBrowser__Cola:Echvi_4222
          Length = 484

 Score =  615 bits (1586), Expect = e-180
 Identities = 285/483 (59%), Positives = 372/483 (77%)

Query: 1   MSVKGDIGVIGLAVMGQNLILNMNDHGFKVVAYNRTTSKVDEFLEGAAKGTNIIGAYSLE 60
           MS   DIG+IGLAVMG+NL+LNM   GF V  YNR+T KVD+F++G   G N IG +S++
Sbjct: 1   MSKLADIGLIGLAVMGENLVLNMESKGFSVAVYNRSTDKVDKFIQGRGAGKNFIGTHSVK 60

Query: 61  DLANKLEKPRKVMLMVRAGEVVDHFIDALLPHLEAGDIIIDGGNSNYPDTNRRVAALREK 120
           +L + L+KPRKVM++V+AG+ VD FI+ ++PHLE GDIIIDGGNSN+ DT RR   +  K
Sbjct: 61  ELVDSLQKPRKVMMLVKAGDPVDSFIEQIIPHLEEGDIIIDGGNSNFTDTIRRTEYVESK 120

Query: 121 GIRFIGTGVSGGEEGARHGPSIMPGGNEEAWQFVKPVLQAISAKTEQGEPCCDWVGKDGA 180
           G +++GTGVSGGE GA  GPS+MPGG++ AW  VK + Q++SAK + G PCCDWVG DGA
Sbjct: 121 GFQYVGTGVSGGEIGALRGPSMMPGGSKSAWPHVKEIFQSVSAKVDGGVPCCDWVGADGA 180

Query: 181 GHFVKMVHNGIEYGDMQLICEAYQFLKEGVGLSDDELQATFNEWRNTELDSYLIDITADI 240
           GH+VKM+HNGIEYGDMQ+I EAYQF+K+ +G+  DE+  TF +W + ELDSYLI+ITADI
Sbjct: 181 GHYVKMIHNGIEYGDMQIITEAYQFMKDVLGMDYDEMHKTFKKWNSEELDSYLIEITADI 240

Query: 241 LGYKDADGSRLVDKVLDTAGQKGTGKWTGINALDFGIPLTLITESVFARCVSAFKDQRVA 300
           L YKD DG  +V+K+LDTAGQKGTGKWTGI A+  G+PLTLI ESVF+R +SA  + R  
Sbjct: 241 LAYKDEDGEPMVEKILDTAGQKGTGKWTGIEAMHLGVPLTLIAESVFSRFLSAQLELRDQ 300

Query: 301 ASKLFHKTIGKVEGDKKVWIEAVRKALLASKIISYAQGFMLIREASEHFNWNINYGNTAL 360
           AS++F       +G+K+  +E ++ A+  +KIISYAQG+ L+ EAS+  NW +NYG+ AL
Sbjct: 301 ASQVFDAPAISFDGNKEAMLEDLKMAVYGAKIISYAQGYNLLMEASKEHNWELNYGDIAL 360

Query: 361 LWREGCIIRSRFLGNIRDAYEANPDLIFLGSDSYFKGILENAMSDWRKVVAKSIEVGIPM 420
           +WR GCIIRS FLG+I+ A++ NP L  L  D +FK  ++NA + WRKV A ++  GIP+
Sbjct: 361 MWRGGCIIRSAFLGDIKKAFDKNPGLPHLLLDDFFKEKVQNAQAGWRKVCAAAVTNGIPV 420

Query: 421 PCMASAITFLDGYTSARLPANLLQAQRDYFGAHTYERTDKPRGEFFHTNWTGRGGNTAST 480
           P +++A+ + DG+ + RLPANLLQAQRDYFGAHTYERTDKPRGEFFHTNWTG G +T ST
Sbjct: 421 PALSAALAYFDGFRTKRLPANLLQAQRDYFGAHTYERTDKPRGEFFHTNWTGEGADTVST 480

Query: 481 TYD 483
            Y+
Sbjct: 481 AYN 483


Lambda     K      H
   0.319    0.137    0.415 

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: 792
Number of extensions: 35
Number of successful extensions: 1
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: 484
Length of database: 484
Length adjustment: 34
Effective length of query: 450
Effective length of database: 450
Effective search space:   202500
Effective search space used:   202500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Echvi_4222 Echvi_4222 (6-phosphogluconate dehydrogenase, decarboxylating)
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.21810.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   6.8e-231  752.9   0.1   7.8e-231  752.7   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4222  Echvi_4222 6-phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4222  Echvi_4222 6-phosphogluconate dehydrogenase, decarboxylating
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  752.7   0.1  7.8e-231  7.8e-231       1     466 [.       6     471 ..       6     472 .. 1.00

  Alignments for each domain:
  == domain 1  score: 752.7 bits;  conditional E-value: 7.8e-231
                            TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilllvkaG 74 
                                          diGliGlavmG+nlvln+++kGfsvavynr+++k+d++++ +  gk+++g++s++e+v+sl+kPrk+++lvkaG
  lcl|FitnessBrowser__Cola:Echvi_4222   6 DIGLIGLAVMGENLVLNMESKGFSVAVYNRSTDKVDKFIQGRGAGKNFIGTHSVKELVDSLQKPRKVMMLVKAG 79 
                                          79************************************************************************ PP

                            TIGR00873  75 aavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayel 148
                                          ++vd++ie+++p+le+gdiiidGGns+++dt+rr++ ++ kg+++vG+GvsGGe Ga++GPs+mpGGsk+a+++
  lcl|FitnessBrowser__Cola:Echvi_4222  80 DPVDSFIEQIIPHLEEGDIIIDGGNSNFTDTIRRTEYVESKGFQYVGTGVSGGEIGALRGPSMMPGGSKSAWPH 153
                                          ************************************************************************** PP

                            TIGR00873 149 vepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWneg 221
                                          v++i+q+++akv+ g pcc+++G+dGaGhyvkm+hnGieygdmq+i+eay+++k++l+++++e++++f++Wn++
  lcl|FitnessBrowser__Cola:Echvi_4222 154 VKEIFQSVSAKVDgGVPCCDWVGADGAGHYVKMIHNGIEYGDMQIITEAYQFMKDVLGMDYDEMHKTFKKWNSE 227
                                          *************99*********************************************************** PP

                            TIGR00873 222 eldsylieitadilkkkdedGkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaa 295
                                          eldsylieitadil++kdedG+p+v+kild+agqkGtGkWt i+a++lGvP+tli+esvf+r+ls++ e r +a
  lcl|FitnessBrowser__Cola:Echvi_4222 228 ELDSYLIEITADILAYKDEDGEPMVEKILDTAGQKGTGKWTGIEAMHLGVPLTLIAESVFSRFLSAQLELRDQA 301
                                          ************************************************************************** PP

                            TIGR00873 296 skllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfld 369
                                          s+++ +p +  ++ +ke+++ed++ a+y +ki+syaqG++ll easke++w+ln+g+ial+wrgGciirs+fl 
  lcl|FitnessBrowser__Cola:Echvi_4222 302 SQVFDAPAISFDG-NKEAMLEDLKMAVYGAKIISYAQGYNLLMEASKEHNWELNYGDIALMWRGGCIIRSAFLG 374
                                          *********9998.9*********************************************************** PP

                            TIGR00873 370 kikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrd 443
                                           ikkaf++np l +lll+++fk+++++aq g+rkv a a+++gipvPalsaal+++dg+rt+rlpanllqaqrd
  lcl|FitnessBrowser__Cola:Echvi_4222 375 DIKKAFDKNPGLPHLLLDDFFKEKVQNAQAGWRKVCAAAVTNGIPVPALSAALAYFDGFRTKRLPANLLQAQRD 448
                                          ************************************************************************** PP

                            TIGR00873 444 yfGahtyertdkprgeffhteWl 466
                                          yfGahtyertdkprgeffht+W+
  lcl|FitnessBrowser__Cola:Echvi_4222 449 YFGAHTYERTDKPRGEFFHTNWT 471
                                          **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (484 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: 10.88
//
[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:

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