GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Azospirillum brasilense Sp245

Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate AZOBR_RS06995 AZOBR_RS06995 ribose-phosphate pyrophosphokinase

Query= curated2:Q8TUT6
         (291 letters)



>FitnessBrowser__azobra:AZOBR_RS06995
          Length = 297

 Score =  142 bits (357), Expect = 1e-38
 Identities = 99/278 (35%), Positives = 140/278 (50%), Gaps = 7/278 (2%)

Query: 14  RRLAEELDAELAPVEEDRFPDGEQIVRVPPELDGTVVVVHSMSPPQDENLVKAIITLDAA 73
           RRLAE L+      E  RFPDGE +VR+P  ++   VV  S+  P D+ LV+  +     
Sbjct: 18  RRLAEALNVPCHIAELHRFPDGESLVRLPEAVE-RAVVYRSLDRPNDK-LVELTLAASVL 75

Query: 74  RENGAEEVIAIVPYMAYSRQDRRFEPGEPVSFRAVARAVSANADALITVD--LHEPGTLK 131
           R +GA E+  + PYMAY RQD  F PGEPVS   V   +    D  + V+  LH   TL 
Sbjct: 76  RRHGATELCLVAPYMAYMRQDAVFRPGEPVSQAVVGDWLGRLFDRFVCVEPHLHRTHTLD 135

Query: 132 YFDV--PAENVSAAEELGKYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLEKK 189
              V  P+  +S A  + + L       D V++GPDE A  L   VA   G+      K+
Sbjct: 136 EVFVGRPSVCLSGAGAIAERLRRDGTAPDAVIVGPDEEAAPLVEVVAGPLGLTALVGRKE 195

Query: 190 RLSGDEVEIH-PKELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALLT 248
           R    +V +  P +  + GR VV+VDD+I +G T+   ARA R  GA ++     HAL  
Sbjct: 196 RRGDRDVTVTLPADAPLAGRPVVIVDDVISSGETIFSCARAARAAGAASVRVFGVHALFD 255

Query: 249 RNAATRLLASGFEDIIATDTVPNPFEKVSVAPPVAEAV 286
              A R  A G    ++ D VP+P   + +A  +A+A+
Sbjct: 256 AAVAARFAAEGLGTPLSCDGVPHPSNDLPLARLIADAL 293


Lambda     K      H
   0.314    0.134    0.370 

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: 201
Number of extensions: 14
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: 291
Length of database: 297
Length adjustment: 26
Effective length of query: 265
Effective length of database: 271
Effective search space:    71815
Effective search space used:    71815
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS06995 AZOBR_RS06995 (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.12199.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-49  154.5   0.0    1.9e-49  154.2   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS06995  AZOBR_RS06995 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS06995  AZOBR_RS06995 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.0   1.9e-49   1.9e-49      10     296 ..      14     294 ..       7     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 1.9e-49
                                 TIGR01251  10 kelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkra 78 
                                                + a+++a++l+++   +e ++F+dgE  vr+ e+v   +++++  s     nd+l+el l+++ l+r 
  lcl|FitnessBrowser__azobra:AZOBR_RS06995  14 ADGARRLAEALNVPCHIAELHRFPDGESLVRLPEAV---ERAVVYRSLD-RPNDKLVELTLAASVLRRH 78 
                                               5668999****************************9...6699966666.69***************** PP

                                 TIGR01251  79 saksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiq...gfFd.vpvenl 143
                                               +a ++ +v+Py++Y Rqd  ++++ep+s  +v++ l  +  dr + v+ H + ++   ++F   p   l
  lcl|FitnessBrowser__azobra:AZOBR_RS06995  79 GATELCLVAPYMAYMRQDAVFRPGEPVSQAVVGDWLGRL-FDRFVCVEPHLHRTHtldEVFVgRPSVCL 146
                                               ***************************************.********99776542227787689999* PP

                                 TIGR01251 144 saspklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegk 211
                                               s++  ++e+l+++  + + v+v PD+ a+  ++ va  lgl   + +KeR  ++ +  + + +  ++g+
  lcl|FitnessBrowser__azobra:AZOBR_RS06995 147 SGAGAIAERLRRDGtAPDAVIVGPDEEAAPLVEVVAGPLGLTALVGRKERRGDRDVTVTLPADAPLAGR 215
                                               ***********998899**********************************888677778999****** PP

                                 TIGR01251 212 dvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklp 280
                                                vvivDD+is+g T+   a++++ +GA +v v  +h++f    + r+a  g+ + ++++ +++      
  lcl|FitnessBrowser__azobra:AZOBR_RS06995 216 PVVIVDDVISSGETIFSCARAARAAGAASVRVFGVHALFDAAVAARFAAEGLGTPLSCDGVPH------ 278
                                               ***************************************************************...... PP

                                 TIGR01251 281 kvseisvapliaeaia 296
                                                 +++ +a lia+a++
  lcl|FitnessBrowser__azobra:AZOBR_RS06995 279 PSNDLPLARLIADALL 294
                                               7888889999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (297 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.41
//
[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