Alignments for a candidate for prs in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Klebsiella michiganensis M5al

Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate BWI76_RS17460 BWI76_RS17460 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__Koxy:BWI76_RS17460
          Length = 315

 Score =  594 bits (1531), Expect = e-174
 Identities = 306/315 (97%), Positives = 309/315 (98%)

Query: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60
           MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC
Sbjct: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60

Query: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120
           APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV
Sbjct: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120

Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180
           GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI
Sbjct: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180

Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240
           AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCV+VDDMIDTGGTLCKAAEALKERG
Sbjct: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVMVDDMIDTGGTLCKAAEALKERG 240

Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAI 300
           AKRVFAYATHPIFSGNA  N++NSVIDE VVCDTIPLT EIKAL  VRTLTLSGMLAEAI
Sbjct: 241 AKRVFAYATHPIFSGNAIQNIKNSVIDEFVVCDTIPLTPEIKALEKVRTLTLSGMLAEAI 300

Query: 301 RRISNEESISAMFEH 315
           RRISNEESISAMFEH
Sbjct: 301 RRISNEESISAMFEH 315


Lambda     K      H
   0.322    0.137    0.386 

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: 461
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: 315
Length of database: 315
Length adjustment: 27
Effective length of query: 288
Effective length of database: 288
Effective search space:    82944
Effective search space used:    82944
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: 48 (23.1 bits)

Align candidate BWI76_RS17460 BWI76_RS17460 (ribose-phosphate pyrophosphokinase)
to HMM TIGR01251 (prs: ribose-phosphate diphosphokinase (EC 2.7.6.1))

# 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.aa/TIGR01251.hmm
# target sequence database:        /tmp/gapView.22901.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01251  [M=309]
Accession:   TIGR01251
Description: ribP_PPkin: ribose-phosphate diphosphokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.6e-130  419.8   0.7   2.9e-130  419.6   0.7    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS17460  BWI76_RS17460 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS17460  BWI76_RS17460 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.6   0.7  2.9e-130  2.9e-130       1     309 []       4     314 ..       4     314 .. 0.99

  Alignments for each domain:
  == domain 1  score: 419.6 bits;  conditional E-value: 2.9e-130
                               TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellll 71 
                                             +k+++g++++ela+++a++l ++lgd+ v +F+dgE++v+i+e+vrg d+fii qst+ap+nd+lmel+++
  lcl|FitnessBrowser__Koxy:BWI76_RS17460   4 MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFII-QSTCAPTNDNLMELVVM 73 
                                             799**************************************************.***************** PP

                               TIGR01251  72 idalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpve 141
                                             +dal+rasa+++taviPy+gYaRqd++++  r pi+ak+va++l+++G+drvltvdlH+eqiqgfFdvpv+
  lcl|FitnessBrowser__Koxy:BWI76_RS17460  74 VDALRRASAGRITAVIPYFGYARQDRRVRsARVPITAKVVADFLSSVGVDRVLTVDLHAEQIQGFFDVPVD 144
                                             ***************************9857**************************************** PP

                               TIGR01251 142 nlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegk 211
                                             n+ +sp l+e++ + +l+n++vvsPD G+v ra+++ak l+ +++aii+K+R+ ++n+ +v++++gdv+g+
  lcl|FitnessBrowser__Koxy:BWI76_RS17460 145 NVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKLLNdTDMAIIDKRRP-RANVSQVMHIIGDVAGR 214
                                             *****************************************9***********.888************** PP

                               TIGR01251 212 dvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklp 280
                                             d+v+vDD+i+TggTl+kaae+Lke+GAk+v+++ath++fsg+A++++++++++e +v++ti+   e k+l+
  lcl|FitnessBrowser__Koxy:BWI76_RS17460 215 DCVMVDDMIDTGGTLCKAAEALKERGAKRVFAYATHPIFSGNAIQNIKNSVIDEFVVCDTIPLtPEiKALE 285
                                             ***************************************************************7668**** PP

                               TIGR01251 281 kvseisvapliaeaiarihenesvsslfd 309
                                             kv++++++ ++aeai+ri+++es+s++f+
  lcl|FitnessBrowser__Koxy:BWI76_RS17460 286 KVRTLTLSGMLAEAIRRISNEESISAMFE 314
                                             ***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (315 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: 00:00:00.01
# Mc/sec: 8.66
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis