Alignments for a candidate for gnd in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Mycolicibacterium vanbaalenii PYR-1

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate WP_011780296.1 MVAN_RS15510 phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating)

Query= BRENDA::Q6NHC5
         (484 letters)



>NCBI__GCF_000015305.1:WP_011780296.1
          Length = 489

 Score =  680 bits (1754), Expect = 0.0
 Identities = 337/483 (69%), Positives = 400/483 (82%), Gaps = 4/483 (0%)

Query: 5   TQLAQIGIVGLAVMGSNLARNFAHKGHTVAVFNRSFEKTQALMDQHGDEGNFIPSATIEE 64
           T  AQIG+ GLAVMGSN+ARNFA  G+TVA+ NRS  KT AL+ +HG EG F+ S TI E
Sbjct: 8   TGTAQIGVTGLAVMGSNIARNFARHGYTVALHNRSIAKTDALLAEHGTEGKFVRSETIAE 67

Query: 65  FVASLEKPRRAIIMVQAGPATDAVINQLADAMDEGDIIIDGGNALYTDTIRRESEIAQRG 124
           F+ +LEKPRR +IMV+AG  TDAVIN+LADAM+EGDIIIDGGNALYTDTIRRE  I +RG
Sbjct: 68  FLDALEKPRRVLIMVKAGDPTDAVINELADAMEEGDIIIDGGNALYTDTIRREKAIRERG 127

Query: 125 LNFVGAGISGGEEGALNGPSIMPGGPDKSWEALGPLLESIAAQVGGTPCVTHIGPDGAGH 184
           L+FVGAGISGGEEGALNGPSIMPGGP +S+E+LGPLLE I+A V G PC THIGPDGAGH
Sbjct: 128 LHFVGAGISGGEEGALNGPSIMPGGPKESYESLGPLLEEISAHVDGVPCCTHIGPDGAGH 187

Query: 185 FVKMVHNGIEYADMQVIGEAYQLLRYATEMQPSEIADVFKTWNQGDLDSYLIEITSEVLA 244
           FVKMVHNGIEY+DMQ+IGEAYQLLR        EIADVF  WN GDLDS+L+EIT++VL 
Sbjct: 188 FVKMVHNGIEYSDMQLIGEAYQLLRDGLGKTAPEIADVFDEWNSGDLDSFLVEITAQVLR 247

Query: 245 QVDSETGTPLIDLIVDEAGQKGTGRWTVKAALDLGIATTGIGEAVFARALSGATTQRKAA 304
           Q D++TG PL+DLI+DEA QKGTGRWTVK+ALDLG+  TGI EAVFARALSG+  QR+A 
Sbjct: 248 QTDAKTGKPLVDLILDEAEQKGTGRWTVKSALDLGVPVTGIAEAVFARALSGSVAQRRAT 307

Query: 305 QGNLPAGTL-ESLASLNIDKDQFVEDVRRALYASKLVAYAQGFDEIIAGSAEHNWDVDPR 363
            G L +G L E + +      QFVED+R+ALYASK++AYAQGF++I AGSAE+NW + P 
Sbjct: 308 TG-LASGRLGERVPADGEAAAQFVEDIRQALYASKIIAYAQGFNQIQAGSAEYNWGITPG 366

Query: 364 DLATIWRGGCIIRAKFLNRIVEAYDANPELPSLLLDPYFKTELESLIDSWRRVVVAATQL 423
           D+ATIWRGGCIIRAKFLNRI +A+D +P+LP+L++DPYF+  +E+ +DSWRRVV+ AT+L
Sbjct: 367 DMATIWRGGCIIRAKFLNRIKDAFDNDPDLPTLIVDPYFRDAIEAAVDSWRRVVIKATEL 426

Query: 424 GLPVPVFASSLSYYDSLRAERLPAALIQGQRDFFGAHTYRRTDKDGS--FHTLWSGDRSE 481
           G+P+P F+S+LSYYD LR ERLPAAL QG RDFFGAHTY R D D +  FHTLWSGDRSE
Sbjct: 427 GIPIPGFSSALSYYDGLRTERLPAALTQGLRDFFGAHTYGRIDTDPTRRFHTLWSGDRSE 486

Query: 482 VEA 484
           VEA
Sbjct: 487 VEA 489


Lambda     K      H
   0.317    0.135    0.393 

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: 803
Number of extensions: 29
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: 484
Length of database: 489
Length adjustment: 34
Effective length of query: 450
Effective length of database: 455
Effective search space:   204750
Effective search space used:   204750
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_011780296.1 MVAN_RS15510 (phosphogluconate dehydrogenase (NADP(+)-dependent, 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.4528.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-217  708.3   0.0   2.5e-217  708.1   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011780296.1  MVAN_RS15510 phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011780296.1  MVAN_RS15510 phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxyla
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.1   0.0  2.5e-217  2.5e-217       1     466 [.      12     481 ..      12     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 708.1 bits;  conditional E-value: 2.5e-217
                                 TIGR00873   1 diGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrkill 69 
                                               +iG++GlavmG+n+++n+a++G++va++nr+ +ktd+ll+e+ ++ k+v++e+i+ef+++lekPr++l+
  lcl|NCBI__GCF_000015305.1:WP_011780296.1  12 QIGVTGLAVMGSNIARNFARHGYTVALHNRSIAKTDALLAEHGTEGKFVRSETIAEFLDALEKPRRVLI 80 
                                               69******************************************************************* PP

                                 TIGR00873  70 lvkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGarkGPslm 138
                                               +vkaG+++davi+el++++e+gdiiidGGn+ly+dt+rrek+++e+g++fvG+G+sGGeeGa++GPs+m
  lcl|NCBI__GCF_000015305.1:WP_011780296.1  81 MVKAGDPTDAVINELADAMEEGDIIIDGGNALYTDTIRREKAIRERGLHFVGAGISGGEEGALNGPSIM 149
                                               ********************************************************************* PP

                                 TIGR00873 139 pGGskeayelvepilqkiaakvegepcceyiGedGaGhyvkmvhnGieygdmqliaeayellkealkls 207
                                               pGG ke+ye++ p+l++i+a+v+g pcc++iG+dGaGh+vkmvhnGiey+dmqli+eay+ll+++l+ +
  lcl|NCBI__GCF_000015305.1:WP_011780296.1 150 PGGPKESYESLGPLLEEISAHVDGVPCCTHIGPDGAGHFVKMVHNGIEYSDMQLIGEAYQLLRDGLGKT 218
                                               ********************************************************************* PP

                                 TIGR00873 208 aeeiaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWtaidaldlGvPvtl 275
                                               a eia+vf+eWn+g+lds+l+eita++l+++d++ Gkplvd ild+a+qkGtG+Wt+++aldlGvPvt 
  lcl|NCBI__GCF_000015305.1:WP_011780296.1 219 APEIADVFDEWNSGDLDSFLVEITAQVLRQTDAKtGKPLVDLILDEAEQKGTGRWTVKSALDLGVPVTG 287
                                               ********************************999********************************** PP

                                 TIGR00873 276 itesvfarvlsslkeervaaskllsgplaeekae...dkeefiedvrealyaskivsyaqGfallkeas 341
                                               i+e+vfar+ls+   +r a++ l sg l e+ +     +++f+ed+r+alyaski++yaqGf++++++s
  lcl|NCBI__GCF_000015305.1:WP_011780296.1 288 IAEAVFARALSGSVAQRRATTGLASGRLGERVPAdgeAAAQFVEDIRQALYASKIIAYAQGFNQIQAGS 356
                                               *********************99999665554442227889**************************** PP

                                 TIGR00873 342 keygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalkkaqkglrkvvakaie 410
                                               +ey+w ++ g++a+iwrgGciir+kfl++ik+af+++p+l +l++++yf+da+++a +++r+vv+ka+e
  lcl|NCBI__GCF_000015305.1:WP_011780296.1 357 AEYNWGITPGDMATIWRGGCIIRAKFLNRIKDAFDNDPDLPTLIVDPYFRDAIEAAVDSWRRVVIKATE 425
                                               ********************************************************************* PP

                                 TIGR00873 411 lgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeffhteWl 466
                                               lgip+P++s+als+ydg+rt+rlpa+l+q++rd+fGahty r+d++  + fht W+
  lcl|NCBI__GCF_000015305.1:WP_011780296.1 426 LGIPIPGFSSALSYYDGLRTERLPAALTQGLRDFFGAHTYGRIDTDPTRRFHTLWS 481
                                               *******************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (489 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: 9.23
//
[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)
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Protein sequences (fasta format)
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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