Alignments for a candidate for prs in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Desulfovibrio vulgaris Miyazaki F

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 8499722 DvMF_0487 ribose-phosphate pyrophosphokinase (RefSeq)

Query= SwissProt::P0A1V6
         (315 letters)



>FitnessBrowser__Miya:8499722
          Length = 312

 Score =  334 bits (857), Expect = 1e-96
 Identities = 167/311 (53%), Positives = 226/311 (72%), Gaps = 3/311 (0%)

Query: 3   DMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAP 62
           D+K+  G + P LA+ I N L   L  A    FSDGE+ ++I +NVRG D+F++Q+TC+P
Sbjct: 4   DLKILTGTSNPALAKAICNHLGCQLTPALCETFSDGEIRIEIGDNVRGDDVFVVQATCSP 63

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

Query: 123 DRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAK 182
           DRV+TVDLHA QIQGFF+VPVDN++  P++LE  L+    + ++VSPD GGV RAR+ AK
Sbjct: 123 DRVVTVDLHAGQIQGFFNVPVDNLYAQPVILE-YLRPYAGDIVIVSPDAGGVERARSFAK 181

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            LN   +AIIDKRR R N +  MH+IGDV  +  ++VDDMIDT GT+C A E L + GAK
Sbjct: 182 KLN-AGLAIIDKRRDRPNQASAMHVIGDVRDKIAIVVDDMIDTAGTMCAAGEVLLKNGAK 240

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302
            V A ATHP+ SG A   L NS   +V+V DT+PL D++ A   ++ L+++G+LA+AI  
Sbjct: 241 EVMACATHPVLSGPAIERLCNSTFSQVIVTDTVPLGDKLAACSKLKVLSVAGLLAKAIHN 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: 296
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 8499722 DvMF_0487 (ribose-phosphate pyrophosphokinase (RefSeq))
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.10308.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-125  404.0   0.0   1.9e-125  403.9   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499722  DvMF_0487 ribose-phosphate pyrop


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499722  DvMF_0487 ribose-phosphate pyrophosphokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.9   0.0  1.9e-125  1.9e-125       2     308 ..       6     311 ..       5     312 .] 0.99

  Alignments for each domain:
  == domain 1  score: 403.9 bits;  conditional E-value: 1.9e-125
                         TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkra 78 
                                       kil g+s+++la++++++lg +l+++  ++F+dgE+ ++i ++vrg dvf++ q t+ pvn +lm+l l++dalkra
  lcl|FitnessBrowser__Miya:8499722   6 KILTGTSNPALAKAICNHLGCQLTPALCETFSDGEIRIEIGDNVRGDDVFVV-QATCSPVNYNLMQLCLMLDALKRA 81 
                                       899*******************************************999999.99999******************* PP

                         TIGR01251  79 saksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkk 155
                                       sa++vtav+PyygYaRqd+k+++r pisaklva++l++aG+drv+tvdlH+ qiqgfF+vpv+nl+a+p+++e+l+ 
  lcl|FitnessBrowser__Miya:8499722  82 SAGRVTAVVPYYGYARQDRKVSPRAPISAKLVADFLTTAGTDRVVTVDLHAGQIQGFFNVPVDNLYAQPVILEYLRP 158
                                       ****************************************************************************8 PP

                         TIGR01251 156 kelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaael 232
                                        ++ ++v+vsPD+G+vera+++akkl++ laii+K+Rd + n+++ ++++gdv +k +++vDD+i+T+gT+++a e+
  lcl|FitnessBrowser__Miya:8499722 159 -YAGDIVIVSPDAGGVERARSFAKKLNAGLAIIDKRRD-RPNQASAMHVIGDVRDKIAIVVDDMIDTAGTMCAAGEV 233
                                       .59***********************************.999*********************************** PP

                         TIGR01251 233 LkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvssl 307
                                       L ++GAk+v+++ath+v+sg+A+erl ++++++vivt+t++  ++  +++k++++sva l+a+ai +ih+++svs l
  lcl|FitnessBrowser__Miya:8499722 234 LLKNGAKEVMACATHPVLSGPAIERLCNSTFSQVIVTDTVPLgDKlAACSKLKVLSVAGLLAKAIHNIHTESSVSVL 310
                                       ******************************************9889******************************9 PP

                         TIGR01251 308 f 308
                                       f
  lcl|FitnessBrowser__Miya:8499722 311 F 311
                                       9 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: 7.48
//
[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