Alignments for a candidate for gnd in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Trichormus variabilis ATCC 29413

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate WP_011319298.1 AVA_RS12800 NADP-dependent phosphogluconate dehydrogenase

Query= BRENDA::P80859
         (469 letters)



>NCBI__GCF_000204075.1:WP_011319298.1
          Length = 476

 Score =  547 bits (1409), Expect = e-160
 Identities = 275/470 (58%), Positives = 351/470 (74%), Gaps = 3/470 (0%)

Query: 1   MSKQQIGVIGLAVMGKNLALNIESRGFSVSVYNRSSSKTEEFL-QEAKGKNVVGTYSIEE 59
           M+ Q  GVIGLAVMG+N+ALN+E  GF ++VYNRS  KT+ F+ Q A G+NV   +++EE
Sbjct: 1   MTLQSFGVIGLAVMGENIALNVERNGFPIAVYNRSREKTDAFMAQRAGGRNVKAAFTLEE 60

Query: 60  FVQSLETPRKILLMVKAGTATDATIQSLLPHLEKDDILIDGGNTYYKDTQRRNKELAESG 119
           FV +LE PRKIL+MV+AG   DA IQ L P L++ DI+IDGGN++++DTQRR +EL  +G
Sbjct: 61  FVAALERPRKILVMVQAGKPVDAVIQQLKPLLDEGDIIIDGGNSWFEDTQRRTQELEPAG 120

Query: 120 IHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVKPILEAISAKVDGEPCTTYIGPDGAGH 179
           + F+G GVSGGEEGAL GPS+MPGG + ++E + PI   I+A+VD  PC TY+GP G+GH
Sbjct: 121 LRFLGMGVSGGEEGALNGPSLMPGGTQSSYEYLSPIFNKIAAQVDDGPCVTYVGPGGSGH 180

Query: 180 YVKMVHNGIEYGDMQLISESYFILKQVLGLSADELHEVFAEWN-KGELDSYLIEITADIF 238
           YVKMVHNGIEYGDMQLI+E+Y +LK   GL A +LHEVFA+WN   EL+S+LIEITA+IF
Sbjct: 181 YVKMVHNGIEYGDMQLIAEAYDLLKTAGGLDAKQLHEVFAQWNTTDELNSFLIEITANIF 240

Query: 239 TKKDEETGKPLVDVILDKAGQKGTGKWTSQSALDLGVPLPIITESVFARFISAMKEERVK 298
              D +T  PLVD+I+D AGQKGTG+WT Q+AL+LGV +P IT +V AR IS++++ER+ 
Sbjct: 241 PYVDPDTKLPLVDLIVDAAGQKGTGRWTVQTALELGVSIPTITAAVNARIISSIRDERIA 300

Query: 299 ASGLLSGPEVKPVTENKEELIEAVRKALFMSKICSYAQGFAQMKAASEEYNWDLKYGEIA 358
           AS  L+GP  K   + K E I  VR AL+ SKICSYAQG A +  AS  +NW+L   E+A
Sbjct: 301 ASKQLTGPSGKYDGDTK-EFINKVRDALYCSKICSYAQGMALLSTASTTFNWNLNLSELA 359

Query: 359 MIFRGGCIIRAAFLQKIKEAYDREPELDNLLLDSYFKNIVESYQGALRQVISLAVAQGVP 418
            I++GGCIIRA FL KIK+A++  P L NLLL   FK  +   Q A R+VI  A   G+P
Sbjct: 360 RIWKGGCIIRAGFLNKIKKAFNENPALPNLLLAPEFKQTILDRQAAWREVIITAAKLGIP 419

Query: 419 VPSFSSALAYYDSYRTAVLPANLIQAQRDYFGAHTYERTDKEGIFHTEWM 468
           VP+FS++L Y+DSYR   LP NL QAQRDYFGAHTY RTDK G FHTEW+
Sbjct: 420 VPAFSASLDYFDSYRRDRLPQNLTQAQRDYFGAHTYLRTDKAGAFHTEWV 469


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: 622
Number of extensions: 27
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: 469
Length of database: 476
Length adjustment: 33
Effective length of query: 436
Effective length of database: 443
Effective search space:   193148
Effective search space used:   193148
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 WP_011319298.1 AVA_RS12800 (NADP-dependent 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.25692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-222  723.0   0.0   9.1e-222  722.8   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011319298.1  AVA_RS12800 NADP-dependent phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011319298.1  AVA_RS12800 NADP-dependent phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.8   0.0  9.1e-222  9.1e-222       2     466 ..       6     469 ..       5     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 722.8 bits;  conditional E-value: 9.1e-222
                                 TIGR00873   2 iGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkilll 70 
                                               +G+iGlavmG+n++ln++++Gf +avynr++ektd++++++a g+++++a ++eefv++le+Prkil++
  lcl|NCBI__GCF_000204075.1:WP_011319298.1   6 FGVIGLAVMGENIALNVERNGFPIAVYNRSREKTDAFMAQRAGGRNVKAAFTLEEFVAALERPRKILVM 74 
                                               8******************************************************************** PP

                                 TIGR00873  71 vkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslmp 139
                                               v+aG++vdavi++l+pll++gdiiidGGns+++dt+rr++el+ +g++f+G+GvsGGeeGa++GPslmp
  lcl|NCBI__GCF_000204075.1:WP_011319298.1  75 VQAGKPVDAVIQQLKPLLDEGDIIIDGGNSWFEDTQRRTQELEPAGLRFLGMGVSGGEEGALNGPSLMP 143
                                               ********************************************************************* PP

                                 TIGR00873 140 GGskeayelvepilqkiaakvegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealklsa 208
                                               GG++++ye+++pi++kiaa+v++ pc++y+G++G+GhyvkmvhnGieygdmqliaeay+llk+a +l+a
  lcl|NCBI__GCF_000204075.1:WP_011319298.1 144 GGTQSSYEYLSPIFNKIAAQVDDGPCVTYVGPGGSGHYVKMVHNGIEYGDMQLIAEAYDLLKTAGGLDA 212
                                               ********************************************************************* PP

                                 TIGR00873 209 eeiaevfeeWne.geldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtl 275
                                               ++++evf++Wn+ +el+s+lieita+i+ + d d   plvd i+daagqkGtG+Wt++ al+lGv + +
  lcl|NCBI__GCF_000204075.1:WP_011319298.1 213 KQLHEVFAQWNTtDELNSFLIEITANIFPYVDPDtKLPLVDLIVDAAGQKGTGRWTVQTALELGVSIPT 281
                                               ***********8579*******************5569******************************* PP

                                 TIGR00873 276 itesvfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivsyaqGfallkeaskey 344
                                               it++v ar++ss+++er+aask+l+gp+ + ++ d++efi++vr+aly+ski+syaqG+all++as+++
  lcl|NCBI__GCF_000204075.1:WP_011319298.1 282 ITAAVNARIISSIRDERIAASKQLTGPSGKYDG-DTKEFINKVRDALYCSKICSYAQGMALLSTASTTF 349
                                               ******************************999.*********************************** PP

                                 TIGR00873 345 gwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaielgi 413
                                               +w+lnl+e+a+iw+gGciir+ fl+kikkaf+enp l nllla+ fk+++ ++q ++r+v+++a++lgi
  lcl|NCBI__GCF_000204075.1:WP_011319298.1 350 NWNLNLSELARIWKGGCIIRAGFLNKIKKAFNENPALPNLLLAPEFKQTILDRQAAWREVIITAAKLGI 418
                                               ********************************************************************* PP

                                 TIGR00873 414 pvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                               pvPa+sa+l+++d+yr++rlp+nl+qaqrdyfGahty rtdk +   fhteW+
  lcl|NCBI__GCF_000204075.1:WP_011319298.1 419 PVPAFSASLDYFDSYRRDRLPQNLTQAQRDYFGAHTYLRTDKAG--AFHTEWV 469
                                               ******************************************99..9*****6 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.03
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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