Alignments for a candidate for deoD in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoD in Klebsiella michiganensis M5al

Align Purine nucleoside phosphorylase 2; Inosine-guanosine phosphorylase; Purine nucleoside phosphorylase II; PNP II; Xanthosine phosphorylase; EC 2.4.2.1 (characterized)
to candidate BWI76_RS20605 BWI76_RS20605 purine-nucleoside phosphorylase

Query= SwissProt::P45563
         (277 letters)



>FitnessBrowser__Koxy:BWI76_RS20605
          Length = 277

 Score =  493 bits (1268), Expect = e-144
 Identities = 245/277 (88%), Positives = 258/277 (93%)

Query: 1   MSQVQFSHNPLFCIDIIKTYKPDFTPRVAFILGSGLGALADQIENAVAISYEKLPGFPVS 60
           MS   FS NP +  DII+ YKPDFTPRVAFILGSGLGALA+QIE+AVAISYEKLPGFPVS
Sbjct: 1   MSDTLFSQNPWYSADIIRGYKPDFTPRVAFILGSGLGALAEQIEDAVAISYEKLPGFPVS 60

Query: 61  TVHGHAGELVLGHLQGVPVVCMKGRGHFYEGRGMTIMTDAIRTFKLLGCELLFCTNAAGS 120
           TVHGHAGELVLG+L GVPV CMKGRGHFYEGRGM +MTDAIRT KLLGCELLFCTNAAGS
Sbjct: 61  TVHGHAGELVLGNLAGVPVACMKGRGHFYEGRGMPVMTDAIRTLKLLGCELLFCTNAAGS 120

Query: 121 LRPEVGAGSLVALKDHINTMPGTPMVGLNDDRFGERFFSLANAYDAEYRALLQKVAKEEG 180
           LRPEVG GSLVAL DHINTMPGTPMVG ND+RFGERFFSLANAYDA+YRA+LQ VA EEG
Sbjct: 121 LRPEVGPGSLVALSDHINTMPGTPMVGPNDERFGERFFSLANAYDADYRAVLQSVAAEEG 180

Query: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVISARHCDLKVVAVSAITNM 240
           FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVI+ARHC LKVVAVSAITN+
Sbjct: 181 FPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVITARHCGLKVVAVSAITNL 240

Query: 241 AEGLSDVKLSHAQTLAAAELSKQNFINLICGFLRKIA 277
           AEGL DVKLSHAQTLAAAELS+QNFINLICGFLRK+A
Sbjct: 241 AEGLGDVKLSHAQTLAAAELSRQNFINLICGFLRKLA 277


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: 393
Number of extensions: 5
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 BWI76_RS20605 BWI76_RS20605 (purine-nucleoside phosphorylase)
to HMM TIGR01699 (xapA: xanthosine phosphorylase (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/TIGR01699.hmm
# target sequence database:        /tmp/gapView.22675.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01699  [M=248]
Accession:   TIGR01699
Description: XAPA: xanthosine phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-157  508.7   0.5   1.5e-157  508.5   0.5    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS20605  BWI76_RS20605 purine-nucleoside 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20605  BWI76_RS20605 purine-nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.5   0.5  1.5e-157  1.5e-157       1     248 []      27     274 ..      27     274 .. 1.00

  Alignments for each domain:
  == domain 1  score: 508.5 bits;  conditional E-value: 1.5e-157
                               TIGR01699   1 rvafilgsglgdlvdqiendvaisyedlpgfpvssvhghagelvlgdlqgvpvvcmkgrghfyegkgmsim 71 
                                             rvafilgsglg+l++qie++vaisye+lpgfpvs+vhghagelvlg+l+gvpv cmkgrghfyeg+gm +m
  lcl|FitnessBrowser__Koxy:BWI76_RS20605  27 RVAFILGSGLGALAEQIEDAVAISYEKLPGFPVSTVHGHAGELVLGNLAGVPVACMKGRGHFYEGRGMPVM 97 
                                             79********************************************************************* PP

                               TIGR01699  72 tdavrtfkllgcellfctnaagslrpevlagslvalkdhintmpgtplvglnddrfgerffslanaydkel 142
                                             tda+rt+kllgcellfctnaagslrpev++gslval dhintmpgtp+vg+nd+rfgerffslanayd+++
  lcl|FitnessBrowser__Koxy:BWI76_RS20605  98 TDAIRTLKLLGCELLFCTNAAGSLRPEVGPGSLVALSDHINTMPGTPMVGPNDERFGERFFSLANAYDADY 168
                                             *********************************************************************** PP

                               TIGR01699 143 radlakvakeedipltegvfvsylgpnfetaaeirmmqiiggdvvgmsvvpevlsaahcdlkvvalsaitn 213
                                             ra l+ va ee++pltegvfvsy+gpnfetaaeirmmqiiggdvvgmsvvpev++a+hc+lkvva+saitn
  lcl|FitnessBrowser__Koxy:BWI76_RS20605 169 RAVLQSVAAEEGFPLTEGVFVSYPGPNFETAAEIRMMQIIGGDVVGMSVVPEVITARHCGLKVVAVSAITN 239
                                             *********************************************************************** PP

                               TIGR01699 214 laeglsdvklsheqtlkaaklakvnfiklieaflk 248
                                             laegl dvklsh+qtl+aa+l+++nfi+li++fl+
  lcl|FitnessBrowser__Koxy:BWI76_RS20605 240 LAEGLGDVKLSHAQTLAAAELSRQNFINLICGFLR 274
                                             *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.59
//
[ok]

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

Downloads

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

Related tools

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