Alignments for a candidate for deoD in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Desulfovibrio vulgaris Miyazaki F

Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate 8500058 DvMF_0821 purine nucleoside phosphorylase (RefSeq)

Query= BRENDA::P00491
         (289 letters)



>FitnessBrowser__Miya:8500058
          Length = 281

 Score =  236 bits (602), Expect = 4e-67
 Identities = 125/259 (48%), Positives = 169/259 (65%), Gaps = 7/259 (2%)

Query: 24  RPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPRSTVPGHAGRLVFGFLNGRACVMMQG 83
           RP+V ++CG+GLGGL D L  A+   Y  +P FP+STV  H GR +FG +     V+ QG
Sbjct: 30  RPRVGVVCGTGLGGLADALADARPLPYSRVPGFPQSTVASHEGRFLFGRIGTVEVVLQQG 89

Query: 84  RFHMYEGYPLWKVTFPVRVFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLPGFSG 143
           R H+YEGY    V   VRV   LGV+ LV+TNAAG LNP+++ GD+MLI DHIN   F+G
Sbjct: 90  RCHLYEGYAPEDVCMGVRVMAALGVEMLVITNAAGALNPRWDAGDLMLITDHIN---FTG 146

Query: 144 QNPLRGPNDERFGDRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFETV 203
           ++PL GPN + +G RFP MS  YD T+ + A+    ++G +  L+ G YV V GP  ET 
Sbjct: 147 RSPLTGPNHDAWGPRFPDMSAPYDATLGRIAMEEAARLGVR--LERGVYVGVPGPQMETP 204

Query: 204 AECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESLEKANHEEVLAA 263
           AE R+ ++LGADAVGMSTV EVI ARH GLRV G S +TNK + D   +++A  EEV+  
Sbjct: 205 AETRMYRQLGADAVGMSTVLEVIAARHMGLRVLGISCLTNKNLPD--CMQEAPLEEVIRV 262

Query: 264 GKQAAQKLEQFVSILMASI 282
             +A  KL + V+ ++  +
Sbjct: 263 AGEAGDKLTRLVAAVVERV 281


Lambda     K      H
   0.321    0.138    0.419 

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: 262
Number of extensions: 12
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: 289
Length of database: 281
Length adjustment: 26
Effective length of query: 263
Effective length of database: 255
Effective search space:    67065
Effective search space used:    67065
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate 8500058 DvMF_0821 (purine nucleoside phosphorylase (RefSeq))
to HMM TIGR01700 (purine nucleoside phosphorylase I, inosine and guanosine-specific (EC 2.4.2.1))

# 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/TIGR01700.hmm
# target sequence database:        /tmp/gapView.19616.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01700  [M=249]
Accession:   TIGR01700
Description: PNPH: purine nucleoside phosphorylase I, inosine and guanosine-specific
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.8e-96  308.4   0.0    2.1e-96  308.1   0.0    1.0  1  lcl|FitnessBrowser__Miya:8500058  DvMF_0821 purine nucleoside phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8500058  DvMF_0821 purine nucleoside phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.1   0.0   2.1e-96   2.1e-96       2     248 ..      33     278 ..      32     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 308.1 bits;  conditional E-value: 2.1e-96
                         TIGR01700   2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfPvrvl 78 
                                       +++++G+GlG la+ + da  l+ys +P fp+stv  h+G+++fG+++ ++vv+ qGr hlyegy  + v++ vrv+
  lcl|FitnessBrowser__Miya:8500058  33 VGVVCGTGLGGLADALADARPLPYSRVPGFPQSTVASHEGRFLFGRIGTVEVVLQQGRCHLYEGYAPEDVCMGVRVM 109
                                       89*************************************************************************** PP

                         TIGR01700  79 kllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkakeiakeldi 155
                                        +lGve+lv+tnaaG++n+ + +Gdlmli+dhin+ +++Pl Gpn++  G+rfpdms  yd  l + a e a +l++
  lcl|FitnessBrowser__Miya:8500058 110 AALGVEMLVITNAAGALNPRWDAGDLMLITDHINFTGRSPLTGPNHDAWGPRFPDMSAPYDATLGRIAMEEAARLGV 186
                                       ***************************************************************************** PP

                         TIGR01700 156 tlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagildaelsdheevlev 232
                                       +l++Gvyv+v GP+ etpae+r++++lGadavGmstv evi+arh Glrvlg+s++tnk      +e+   eev++v
  lcl|FitnessBrowser__Miya:8500058 187 RLERGVYVGVPGPQMETPAETRMYRQLGADAVGMSTVLEVIAARHMGLRVLGISCLTNKNLPDCMQEAP-LEEVIRV 262
                                       ***********************************************************9965555555.89***** PP

                         TIGR01700 233 akkakekleklvsalv 248
                                       a +a +kl++lv+a+v
  lcl|FitnessBrowser__Miya:8500058 263 AGEAGDKLTRLVAAVV 278
                                       *************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (281 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.57
//
[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