GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoD in Coprobacter fastidiosus NSB1

Align Purine nucleoside phosphorylase 1; PNP 1; Inosine phosphorylase; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase I; PNP I; Pu-NPase I; EC 2.4.2.1 (characterized)
to candidate WP_022601312.1 NSB1T_RS23310 purine-nucleoside phosphorylase

Query= SwissProt::P77834
         (274 letters)



>NCBI__GCF_000473955.1:WP_022601312.1
          Length = 270

 Score =  275 bits (703), Expect = 8e-79
 Identities = 134/263 (50%), Positives = 186/263 (70%)

Query: 6   IEQAAQFLKEKFPTSPQIGLILGSGLGVLADEIEQAIKIPYSDIPNFPVSTVEGHAGQLV 65
           I++ A F+KE+FP  P+  +ILG+GLG L + I    ++ Y DIPNFP+STVEGH+G+L+
Sbjct: 5   IKETAAFIKERFPIIPETAIILGTGLGELVNHITNQKELAYKDIPNFPISTVEGHSGKLI 64

Query: 66  YGQLEGATVVVMQGRFHYYEGYSFDKVTFPVRVMKALGVEQLIVTNAAGGVNESFEPGDL 125
           +G+L    ++ MQGRFH+YEGY   +VTFPVRVMK LGV+ L V+NAAGG+N +F+ GDL
Sbjct: 65  FGKLGTKDIMAMQGRFHFYEGYDMKQVTFPVRVMKQLGVKTLFVSNAAGGMNPTFKVGDL 124

Query: 126 MIISDHINNMGGNPLIGPNDSALGVRFPDMSEAYSKRLRQLAKDVANDIGLRVREGVYVA 185
           M+I DHIN    +PL G N + LG RFPDMSEAYSKRL + A ++A    + +++GVYV 
Sbjct: 125 MVIRDHINLFPEHPLHGKNYNELGPRFPDMSEAYSKRLIKKAFEIAEKNNIYLQQGVYVG 184

Query: 186 NTGPAYETPAEIRMIRVMGGDAVGMSTVPEVIVARHAGMEVLGISCISNMAAGILDQPLT 245
             GP +ETPAE +  +++GGDAVGMSTVPEVIVARH+ MEV  IS I+++    + +  +
Sbjct: 185 TQGPTFETPAEYKYFKIIGGDAVGMSTVPEVIVARHSDMEVFAISVITDLGVEGIVEKAS 244

Query: 246 HDEVIETTEKVKADFLRFVKAIV 268
           H+EV +     +      +K +V
Sbjct: 245 HEEVQKAAALAQPKMTLIMKELV 267


Lambda     K      H
   0.319    0.137    0.388 

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: 250
Number of extensions: 4
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: 274
Length of database: 270
Length adjustment: 25
Effective length of query: 249
Effective length of database: 245
Effective search space:    61005
Effective search space used:    61005
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate WP_022601312.1 NSB1T_RS23310 (purine-nucleoside phosphorylase)
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.975633.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-109  349.8   1.2   4.8e-109  349.6   1.2    1.0  1  NCBI__GCF_000473955.1:WP_022601312.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000473955.1:WP_022601312.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.6   1.2  4.8e-109  4.8e-109       2     248 ..      22     267 ..      21     268 .. 0.98

  Alignments for each domain:
  == domain 1  score: 349.6 bits;  conditional E-value: 4.8e-109
                             TIGR01700   2 iaiilGsGlGelaekvedavildyseiPefpestveGhkGklvfGklegkkvvilqGrfhlyegydlakvtfP 74 
                                           +aiilG+GlGel++++++++ l y++iP+fp stveGh+Gkl+fGkl+ k ++++qGrfh+yegyd+++vtfP
  NCBI__GCF_000473955.1:WP_022601312.1  22 TAIILGTGLGELVNHITNQKELAYKDIPNFPISTVEGHSGKLIFGKLGTKDIMAMQGRFHFYEGYDMKQVTFP 94 
                                           79*********************************************************************** PP

                             TIGR01700  75 vrvlkllGvealvvtnaaGgintefkvGdlmlikdhinllalnPliGpneekfGarfpdmsdaydkelrqkak 147
                                           vrv+k+lGv++l+v+naaGg+n++fkvGdlm+i+dhinl +  Pl G n +++G+rfpdms+ay k l++ka 
  NCBI__GCF_000473955.1:WP_022601312.1  95 VRVMKQLGVKTLFVSNAAGGMNPTFKVGDLMVIRDHINLFPEHPLHGKNYNELGPRFPDMSEAYSKRLIKKAF 167
                                           ************************************************************************* PP

                             TIGR01700 148 eiakelditlkeGvyvavtGPsyetpaevrllkklGadavGmstvpevivarhcGlrvlglslitnkaagild 220
                                           eia++ +i l++Gvyv+ +GP +etpae++ +k +G+davGmstvpevivarh+ + v+++s+it+ +++ + 
  NCBI__GCF_000473955.1:WP_022601312.1 168 EIAEKNNIYLQQGVYVGTQGPTFETPAEYKYFKIIGGDAVGMSTVPEVIVARHSDMEVFAISVITDLGVEGIV 240
                                           *******************************************************************998777 PP

                             TIGR01700 221 aelsdheevlevakkakekleklvsalv 248
                                           +++s heev ++a  a+ k++ ++++lv
  NCBI__GCF_000473955.1:WP_022601312.1 241 EKAS-HEEVQKAAALAQPKMTLIMKELV 267
                                           8888.9*****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (270 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.33
//
[ok]

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

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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:

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:

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:

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:

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