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 (EC 2.4.2.1) (characterized)
to candidate BWI76_RS04145 BWI76_RS04145 purine-nucleoside phosphorylase

Query= BRENDA::P0ABP8
         (239 letters)



>FitnessBrowser__Koxy:BWI76_RS04145
          Length = 240

 Score =  448 bits (1153), Expect = e-131
 Identities = 226/240 (94%), Positives = 233/240 (97%), Gaps = 1/240 (0%)

Query: 1   MATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISV 60
           MATPHINAEMGDFADVVLMPGDPLRAK+IAETFLED REVNNVRGMLGFTGTYKGRKISV
Sbjct: 1   MATPHINAEMGDFADVVLMPGDPLRAKHIAETFLEDVREVNNVRGMLGFTGTYKGRKISV 60

Query: 61  MGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIR 120
           MGHGMGIPSCSIY KELITDFGVKKIIRVGSCGAV   VKLRDVVIGMGACTDSKVNR+R
Sbjct: 61  MGHGMGIPSCSIYAKELITDFGVKKIIRVGSCGAVRMDVKLRDVVIGMGACTDSKVNRMR 120

Query: 121 FKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPD-GEMFDVMEKYGILGV 179
           FKDHDFAAIADF MVRNAVDAAKALG+DARVGN+FSADLFY+PD GEMFDVMEKYGILGV
Sbjct: 121 FKDHDFAAIADFGMVRNAVDAAKALGVDARVGNIFSADLFYAPDGGEMFDVMEKYGILGV 180

Query: 180 EMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDKE 239
           EMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQT++AERQTTFNDMIKIALESVLLGDKE
Sbjct: 181 EMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTSSAERQTTFNDMIKIALESVLLGDKE 240


Lambda     K      H
   0.322    0.138    0.401 

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: 367
Number of extensions: 9
Number of successful extensions: 2
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: 239
Length of database: 240
Length adjustment: 23
Effective length of query: 216
Effective length of database: 217
Effective search space:    46872
Effective search space used:    46872
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: 46 (22.3 bits)

Align candidate BWI76_RS04145 BWI76_RS04145 (purine-nucleoside phosphorylase)
to HMM TIGR00107 (deoD: purine nucleoside 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/TIGR00107.hmm
# target sequence database:        /tmp/gapView.8421.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00107  [M=232]
Accession:   TIGR00107
Description: deoD: purine nucleoside 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.5e-128  411.3   1.0   6.2e-128  411.1   1.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04145  BWI76_RS04145 purine-nucleoside 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04145  BWI76_RS04145 purine-nucleoside phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.1   1.0  6.2e-128  6.2e-128       1     230 [.       5     235 ..       5     237 .. 0.99

  Alignments for each domain:
  == domain 1  score: 411.1 bits;  conditional E-value: 6.2e-128
                               TIGR00107   1 hinakkgdiadvvllpGdPlrakyiaekfledakevnevrgmlgftGkykgkkisvmGhGmGipsisiysk 71 
                                             hina++gd+advvl+pGdPlrak+iae+fled++evn+vrgmlgftG+ykg+kisvmGhGmGips+siy+k
  lcl|FitnessBrowser__Koxy:BWI76_RS04145   5 HINAEMGDFADVVLMPGDPLRAKHIAETFLEDVREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYAK 75 
                                             9********************************************************************** PP

                               TIGR00107  72 elikeyevkkiirvGsCGairkkvklkdviialkastdskvnrvrfvevdlaaiadfelvklakeaakkkg 142
                                             eli++++vkkiirvGsCGa+r++vkl+dv+i+++a+tdskvnr+rf+++d+aaiadf +v++a++aak++g
  lcl|FitnessBrowser__Koxy:BWI76_RS04145  76 ELITDFGVKKIIRVGSCGAVRMDVKLRDVVIGMGACTDSKVNRMRFKDHDFAAIADFGMVRNAVDAAKALG 146
                                             *********************************************************************** PP

                               TIGR00107 143 ldvkvGnvfsadlfystd.kevldllekygvlavemeaaalyavaaelgkkaltlltvsdhlvthealtae 212
                                             +d++vGn+fsadlfy +d  e++d++ekyg+l+vemeaa++y+vaae+g+kalt++tvsdh++the+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS04145 147 VDARVGNIFSADLFYAPDgGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTSSA 217
                                             ****************98459************************************************** PP

                               TIGR00107 213 erqktfkdmielalesvs 230
                                             erq+tf+dmi++alesv+
  lcl|FitnessBrowser__Koxy:BWI76_RS04145 218 ERQTTFNDMIKIALESVL 235
                                             ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (232 nodes)
Target sequences:                          1  (240 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: 6.50
//
[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