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 phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate Echvi_2861 Echvi_2861 6-phosphogluconate dehydrogenase, decarboxylating

Query= BRENDA::P80859
         (469 letters)



>FitnessBrowser__Cola:Echvi_2861
          Length = 465

 Score =  479 bits (1234), Expect = e-140
 Identities = 241/468 (51%), Positives = 328/468 (70%), Gaps = 5/468 (1%)

Query: 1   MSKQQIGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFLQEAK-GKNVVGTYSIEE 59
           M +   G++GL VMGKNL LN+   GFSV+  +   +K     + A+ G++V G  + E+
Sbjct: 1   MKQFDFGIVGLGVMGKNLLLNMADHGFSVAGLDLDQAKAAALEEGAREGQDVKGFITAEK 60

Query: 60  FVQSLETPRKILLMVKAGTATDATIQSLLPHLEKDDILIDGGNTYYKDTQRRNKELAESG 119
           FV SL+ PR I+L+V AG   DA I SLLP LEKDDI++DGGN+Y+ DT+RR  ELA+  
Sbjct: 61  FVSSLKRPRAIMLLVPAGKPVDAAIGSLLPLLEKDDIVVDGGNSYFPDTERRFAELAKKN 120

Query: 120 IHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKVDGEPCTTYIGPDGAGH 179
           IHF G G+SGGE+GA  GPS+MPGG  +A+E ++PI EAI+AKVDGEPC TY+G   AG+
Sbjct: 121 IHFFGMGISGGEKGARFGPSMMPGGDAQAYERLRPIFEAIAAKVDGEPCVTYLGKGSAGN 180

Query: 180 YVKMVHNGIEYGDMQLISESYFILKQVLGLSADELHEVFAEWNKGELDSYLIEITADIFT 239
           YVKMVHNGIEYG MQLI+E+Y I+K+ LG S D++  +FA WN  EL S+L+EIT  I  
Sbjct: 181 YVKMVHNGIEYGIMQLIAETYDIMKKGLGYSDDKIQSIFASWNDTELQSFLVEITGLILQ 240

Query: 240 KKDEETGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPIITESVFARFISAMKEERVKA 299
           KKD++TGK L+ +I D+A  KGTGKWTSQ+A+DL  P+P+I  +V  R IS  KEERV A
Sbjct: 241 KKDDDTGKQLLPLISDQARSKGTGKWTSQNAMDLQAPVPVIDMAVLMRDISKFKEERVAA 300

Query: 300 SGLLSGPEVKPVTENKEELIEAVRKALFMSKICSYAQGFAQMKAASEEYNWDLKYGEIAM 359
           S  L         EN +   + ++ AL+   I +YAQG  Q++ ASEEY + L   E+A 
Sbjct: 301 SKALKWAG----EENVDATADMLKNALYFGMITTYAQGMVQLRLASEEYGYGLNLEEVAK 356

Query: 360 IFRGGCIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVESYQGALRQVISLAVAQGVPV 419
           I+RGGCIIRAA L+  ++AY + P+L NL+LD      + + Q  +R+V+ +AV +G+P 
Sbjct: 357 IWRGGCIIRAACLEDFRKAYKKAPDLANLMLDKEIGEDLVARQKDVREVVKVAVEKGIPA 416

Query: 420 PSFSSALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDKEGIFHTEW 467
           P+  +AL+Y+D+YR+  L  N+IQAQRD+FGAH +ER DKEG+FH +W
Sbjct: 417 PALMAALSYFDAYRSDRLSTNVIQAQRDFFGAHQFERIDKEGVFHAQW 464


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: 599
Number of extensions: 19
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: 469
Length of database: 465
Length adjustment: 33
Effective length of query: 436
Effective length of database: 432
Effective search space:   188352
Effective search space used:   188352
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 Echvi_2861 Echvi_2861 (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.13148.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-185  603.0   0.1   2.1e-185  602.9   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2861  Echvi_2861 6-phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2861  Echvi_2861 6-phosphogluconate dehydrogenase, decarboxylating
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.9   0.1  2.1e-185  2.1e-185       1     465 [.       5     464 ..       5     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 602.9 bits;  conditional E-value: 2.1e-185
                            TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilllvkaG 74 
                                          d+G++Gl+vmGknl+ln+ad+Gfsva  + +++k+ +l + + +g++++g+ + e+fv+sl++Pr i+llv aG
  lcl|FitnessBrowser__Cola:Echvi_2861   5 DFGIVGLGVMGKNLLLNMADHGFSVAGLDLDQAKAAALEEGAREGQDVKGFITAEKFVSSLKRPRAIMLLVPAG 78 
                                          79************************************************************************ PP

                            TIGR00873  75 aavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmpGGskeayel 148
                                          ++vda+i +llpllek di++dGGns+++dterr  el++k+i+f G+G+sGGe+Gar+GPs+mpGG+++aye 
  lcl|FitnessBrowser__Cola:Echvi_2861  79 KPVDAAIGSLLPLLEKDDIVVDGGNSYFPDTERRFAELAKKNIHFFGMGISGGEKGARFGPSMMPGGDAQAYER 152
                                          ************************************************************************** PP

                            TIGR00873 149 vepilqkiaakvegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsaeeiaevfeeWnege 222
                                          ++pi+++iaakv+gepc++y+G++ aG yvkmvhnGieyg mqliae+y+++k++l+ s+++i+++f+ Wn++e
  lcl|FitnessBrowser__Cola:Echvi_2861 153 LRPIFEAIAAKVDGEPCVTYLGKGSAGNYVKMVHNGIEYGIMQLIAETYDIMKKGLGYSDDKIQSIFASWNDTE 226
                                          ************************************************************************** PP

                            TIGR00873 223 ldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtlitesvfarvlsslkeervaa 295
                                          l+s+l+eit  il+kkd+d Gk+l+  i d+a  kGtGkWt+++a+dl  Pv +i  +v+ r +s +keervaa
  lcl|FitnessBrowser__Cola:Echvi_2861 227 LQSFLVEITGLILQKKDDDtGKQLLPLISDQARSKGTGKWTSQNAMDLQAPVPVIDMAVLMRDISKFKEERVAA 300
                                          ****************9999****************************************************** PP

                            TIGR00873 296 skllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskeygwdlnlgeialiwrgGciirskfld 369
                                          sk l+   +e+     ++  + +++aly + i +yaqG+ +l+ as+eyg+ lnl+e+a+iwrgGciir++ l+
  lcl|FitnessBrowser__Cola:Echvi_2861 301 SKALKWAGEEN----VDATADMLKNALYFGMITTYAQGMVQLRLASEEYGYGLNLEEVAKIWRGGCIIRAACLE 370
                                          **998755443....45677899*************************************************** PP

                            TIGR00873 370 kikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrd 443
                                            +ka+++ p+l+nl+l++   + l ++qk++r+vv  a+e+gip Pal aals++d+yr++rl++n++qaqrd
  lcl|FitnessBrowser__Cola:Echvi_2861 371 DFRKAYKKAPDLANLMLDKEIGEDLVARQKDVREVVKVAVEKGIPAPALMAALSYFDAYRSDRLSTNVIQAQRD 444
                                          ************************************************************************** PP

                            TIGR00873 444 yfGahtyertdkprgeffhteW 465
                                          +fGah +er+dk++  +fh++W
  lcl|FitnessBrowser__Cola:Echvi_2861 445 FFGAHQFERIDKEG--VFHAQW 464
                                          ************99..****** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (465 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: 00:00:00.01
# Mc/sec: 12.27
//
[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