GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Desulfovibrio vulgaris Hildenborough

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 207025 DVU1575 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>MicrobesOnline__882:207025
          Length = 312

 Score =  337 bits (864), Expect = 2e-97
 Identities = 167/311 (53%), Positives = 228/311 (73%), Gaps = 3/311 (0%)

Query: 3   DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62
           D+K+  G + PELA+ I N L   +  A    FSDGE+ ++I +NVRG D+F++Q+TCAP
Sbjct: 4   DLKILTGTSNPELAKAICNHLGCQITPALCETFSDGEIRIEIGDNVRGDDVFVVQATCAP 63

Query: 63  TNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGV 122
            N NLM+L +M+DAL+RASAGR+TAV+PY+GYARQDR+V S R PI+AK+VADFL++ G 
Sbjct: 64  VNFNLMQLFLMLDALKRASAGRVTAVMPYYGYARQDRKV-SPRAPISAKLVADFLTTAGT 122

Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182
           DRV+TVDLHA QIQGFF+ PVDN++ +P++L+ + Q+     ++VSPD GGV RARA AK
Sbjct: 123 DRVVTVDLHAGQIQGFFNSPVDNLYAAPVILDYLRQVE-GEIVIVSPDAGGVERARAYAK 181

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            LN   +AI+DKRR + N +Q MH+IGDV  +  ++VDDMIDT GTLC A E L + GA+
Sbjct: 182 RLN-AGLAIVDKRRDKPNQAQAMHVIGDVRDKVAIVVDDMIDTAGTLCAAGEVLLKNGAR 240

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302
            V A ATHP+ SG A   L NS   +V+V DT+PL D++ A P +  L+++G+LA+AI  
Sbjct: 241 EVMACATHPVLSGPAIERLCNSPFKQVIVTDTVPLGDKLNACPKLHVLSVAGLLAKAIHN 300

Query: 303 ISNEESISAMF 313
           I  E S+S +F
Sbjct: 301 IHTESSVSVLF 311


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: 306
Number of extensions: 10
Number of successful extensions: 4
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: 312
Length adjustment: 27
Effective length of query: 288
Effective length of database: 285
Effective search space:    82080
Effective search space used:    82080
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 207025 DVU1575 (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.20740.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.5e-124  400.8   0.0   1.7e-124  400.7   0.0    1.0  1  lcl|MicrobesOnline__882:207025  DVU1575 ribose-phosphate pyropho


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207025  DVU1575 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.7   0.0  1.7e-124  1.7e-124       2     308 ..       6     311 ..       5     312 .] 0.99

  Alignments for each domain:
  == domain 1  score: 400.7 bits;  conditional E-value: 1.7e-124
                       TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasa 80 
                                     kil g+s++ela++++++lg +++++  ++F+dgE+ ++i ++vrg dvf++ q t+apvn +lm+l l++dalkrasa
  lcl|MicrobesOnline__882:207025   6 KILTGTSNPELAKAICNHLGCQITPALCETFSDGEIRIEIGDNVRGDDVFVV-QATCAPVNFNLMQLFLMLDALKRASA 83 
                                     899*******************************************999999.************************** PP

                       TIGR01251  81 ksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelk 159
                                     ++vtav+PyygYaRqd+k+++r pisaklva++l++aG+drv+tvdlH+ qiqgfF+ pv+nl+a+p+++++l++ +  
  lcl|MicrobesOnline__882:207025  84 GRVTAVMPYYGYARQDRKVSPRAPISAKLVADFLTTAGTDRVVTVDLHAGQIQGFFNSPVDNLYAAPVILDYLRQ-VEG 161
                                     **************************************************************************8.599 PP

                       TIGR01251 160 nlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGA 238
                                     ++v+vsPD+G+vera+++ak+l++ lai++K+Rd k n+++ ++++gdv +k +++vDD+i+T+gTl++a e+L ++GA
  lcl|MicrobesOnline__882:207025 162 EIVIVSPDAGGVERARAYAKRLNAGLAIVDKRRD-KPNQAQAMHVIGDVRDKVAIVVDDMIDTAGTLCAAGEVLLKNGA 239
                                     **********************************.999***************************************** PP

                       TIGR01251 239 kkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                     ++v+++ath+v+sg+A+erl ++ +++vivt+t++  ++ +++pk++++sva l+a+ai +ih+++svs lf
  lcl|MicrobesOnline__882:207025 240 REVMACATHPVLSGPAIERLCNSPFKQVIVTDTVPLgDKlNACPKLHVLSVAGLLAKAIHNIHTESSVSVLF 311
                                     ************************************9889******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (312 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: 7.35
//
[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:

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