Alignments for a candidate for deoD in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Azospirillum brasilense Sp245

Align Purine nucleoside phosphorylase 2; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase II; PNP II; Xanthosine phosphorylase; EC 2.4.2.1 (characterized)
to candidate AZOBR_RS06645 AZOBR_RS06645 purine nucleoside phosphorylase

Query= SwissProt::P45563
         (277 letters)



>FitnessBrowser__azobra:AZOBR_RS06645
          Length = 277

 Score =  269 bits (688), Expect = 4e-77
 Identities = 132/252 (52%), Positives = 168/252 (66%)

Query: 22  PDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVSTVHGHAGELVLGHLQGVPVVC 81
           P F PRV  +LGSGLG +AD+IE A  + Y  LPGFP+ +V GH G LVLGHL G PV C
Sbjct: 15  PGFRPRVGIVLGSGLGGVADRIEGATVMPYGDLPGFPLPSVEGHMGRLVLGHLGGQPVAC 74

Query: 82  MKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGSLRPEVGAGSLVALKDHINTMP 141
           M+GR H YEG G   +  A+R  KL GC+ L  T AAGSLR EVG G L+A+ DHIN + 
Sbjct: 75  MQGRVHAYEGNGFDALKTAVRALKLAGCDTLVLTCAAGSLRVEVGPGRLMAISDHINMLG 134

Query: 142 GTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEGFPLTEGVFVSYPGPNFETAAE 201
             P+ G N+D FG RF S+ +A+D   RAL+++ A E    L EGV+ +YPGP+FET AE
Sbjct: 135 ANPLTGPNEDSFGPRFPSMTDAWDPALRALMRRRALELNIDLVEGVYAAYPGPSFETPAE 194

Query: 202 IRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNMAEGLSDVKLSHAQTLAAAELS 261
           +RM++++G D VGMS VPE I ARHC L+VV  + ITN+  GL D  + H QTL AA  +
Sbjct: 195 VRMLKVLGADAVGMSTVPECIVARHCGLRVVGCAVITNLGVGLGDGPVDHDQTLRAASAA 254

Query: 262 KQNFINLICGFL 273
             +   L+ GFL
Sbjct: 255 ASDLERLLTGFL 266


Lambda     K      H
   0.323    0.139    0.410 

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: 292
Number of extensions: 17
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: 277
Length of database: 277
Length adjustment: 25
Effective length of query: 252
Effective length of database: 252
Effective search space:    63504
Effective search space used:    63504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate AZOBR_RS06645 AZOBR_RS06645 (purine nucleoside phosphorylase)
to HMM TIGR01697 (inosine/guanosine/xanthosine phosphorylase family (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/TIGR01697.hmm
# target sequence database:        /tmp/gapView.26686.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01697  [M=247]
Accession:   TIGR01697
Description: PNPH-PUNA-XAPA: inosine/guanosine/xanthosine phosphorylase family
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-102  325.6   0.0     1e-101  325.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS06645  AZOBR_RS06645 purine nucleoside 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS06645  AZOBR_RS06645 purine nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.5   0.0    1e-101    1e-101       1     245 [.      20     265 ..      20     267 .. 0.99

  Alignments for each domain:
  == domain 1  score: 325.5 bits;  conditional E-value: 1e-101
                                 TIGR01697   1 kvaiilGsGlgsladkvedavvipyeeiPgFpvstveGHagelvfgklggkkvvvlaGRfHlYegydla 69 
                                               +v+i+lGsGlg +ad++e a+v+py ++PgFp ++veGH g+lv+g+lgg++v +++GR+H Yeg+  +
  lcl|FitnessBrowser__azobra:AZOBR_RS06645  20 RVGIVLGSGLGGVADRIEGATVMPYGDLPGFPLPSVEGHMGRLVLGHLGGQPVACMQGRVHAYEGNGFD 88 
                                               599****************************************************************** PP

                                 TIGR01697  70 avtlpvrvlkllGvkvlvvtnaaGglnkelkvGdlvlikDhinlsglnplvGpndeefGtrFvdlsnay 138
                                               a++++vr+lkl G+ +lv+t aaG+l+ e+ +G l++i+Dhin+ g npl Gpn+++fG rF+++++a+
  lcl|FitnessBrowser__azobra:AZOBR_RS06645  89 ALKTAVRALKLAGCDTLVLTCAAGSLRVEVGPGRLMAISDHINMLGANPLTGPNEDSFGPRFPSMTDAW 157
                                               ********************************************************************* PP

                                 TIGR01697 139 dkelrklvkdvakekdvslkeGvyvlvsGPsyetpaeirllkllGaDvvGmstvpevivarhcGikvla 207
                                               d++lr+l++  a e +++l eGvy++++GPs+etpae+r+lk+lGaD+vGmstvpe ivarhcG++v++
  lcl|FitnessBrowser__azobra:AZOBR_RS06645 158 DPALRALMRRRALELNIDLVEGVYAAYPGPSFETPAEVRMLKVLGADAVGMSTVPECIVARHCGLRVVG 226
                                               ********************************************************************* PP

                                 TIGR01697 208 vslvtnlaag.ldeelsheevlevakaaaekleklleei 245
                                                +++tnl++g  d +++h+++l++a+aaa++le+ll+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS06645 227 CAVITNLGVGlGDGPVDHDQTLRAASAAASDLERLLTGF 265
                                               **********99**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (247 nodes)
Target sequences:                          1  (277 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: 11.16
//
[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