GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Paraburkholderia bryophila 376MFSha3.1

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate H281DRAFT_01939 H281DRAFT_01939 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__Burk376:H281DRAFT_01939
          Length = 318

 Score =  404 bits (1038), Expect = e-117
 Identities = 195/310 (62%), Positives = 250/310 (80%), Gaps = 1/310 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           + +F GNA P LAQ +   L   LG A V RFSDGE+ V+I ENVRG D+F++QSTCAP 
Sbjct: 7   LMVFTGNANPALAQEVVKILGIPLGKAMVSRFSDGEIQVEIQENVRGKDVFVLQSTCAPA 66

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMEL++MVDAL+RASAGRITA IPYFGYARQDRR RSARV I+AK+VA+ L   GV+
Sbjct: 67  NDNLMELMIMVDALKRASAGRITAAIPYFGYARQDRRPRSARVAISAKIVANMLEIAGVE 126

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183
           R++T+DLHA+QIQGFFD+PVDN++ +P+LL D+ + N +N +VVSPD+GGVVRARA+AK 
Sbjct: 127 RIITMDLHADQIQGFFDIPVDNIYATPVLLGDLRKQNYENLLVVSPDVGGVVRARALAKQ 186

Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243
           LN  D+AIIDKRRP+ANV++VM+IIG+V GR CV++DDM+DT GTLCKAA+ LKERGAK+
Sbjct: 187 LN-CDLAIIDKRRPKANVAEVMNIIGEVEGRTCVIMDDMVDTAGTLCKAAQVLKERGAKQ 245

Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303
           VFAYATHP+ SG A   +  S +DE+VV DTIPL +E +S   +R+LT +G+LAE   RI
Sbjct: 246 VFAYATHPVLSGGAGERIAASALDELVVTDTIPLGEEARSCAKIRSLTSAGLLAETFSRI 305

Query: 304 SNEESISAMF 313
              +S+ ++F
Sbjct: 306 RRGDSVMSLF 315


Lambda     K      H
   0.321    0.137    0.385 

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: 310
Number of extensions: 10
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: 315
Length of database: 318
Length adjustment: 27
Effective length of query: 288
Effective length of database: 291
Effective search space:    83808
Effective search space used:    83808
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 H281DRAFT_01939 H281DRAFT_01939 (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.27893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-125  403.8   0.2   2.3e-125  403.6   0.2    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01939  H281DRAFT_01939 ribose-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01939  H281DRAFT_01939 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.6   0.2  2.3e-125  2.3e-125       2     308 ..       8     315 ..       7     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 403.6 bits;  conditional E-value: 2.3e-125
                                    TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalme 67 
                                                  +++ g+++++la++v k lg++lg++ v +F+dgE++v+i+e+vrgkdvf++ qst+ap nd+lme
  lcl|FitnessBrowser__Burk376:H281DRAFT_01939   8 MVFTGNANPALAQEVVKILGIPLGKAMVSRFSDGEIQVEIQENVRGKDVFVL-QSTCAPANDNLME 72 
                                                  89**************************************************.************* PP

                                    TIGR01251  68 llllidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqi 132
                                                  l++++dalkrasa+++ta iPy+gYaRqd++ +  r +isak+va++le aG++r++t+dlH++qi
  lcl|FitnessBrowser__Burk376:H281DRAFT_01939  73 LMIMVDALKRASAGRITAAIPYFGYARQDRRPRsARVAISAKIVANMLEIAGVERIITMDLHADQI 138
                                                  ******************************97758******************************* PP

                                    TIGR01251 133 qgfFdvpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskene 198
                                                  qgfFd+pv+n++a p+l+ +l+k++ +nl+vvsPD G+v ra+++ak+l+++laii+K+R+ k+n+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01939 139 QGFFDIPVDNIYATPVLLGDLRKQNYENLLVVSPDVGGVVRARALAKQLNCDLAIIDKRRP-KANV 203
                                                  *************************************************************.899* PP

                                    TIGR01251 199 vevtnllgdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagve 264
                                                  +ev+n++g+veg+++vi+DD+++T+gTl+kaa++Lke+GAk+v+++ath+v+sg A er+a + ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01939 204 AEVMNIIGEVEGRTCVIMDDMVDTAGTLCKAAQVLKERGAKQVFAYATHPVLSGGAGERIAASALD 269
                                                  ****************************************************************** PP

                                    TIGR01251 265 evivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                                  e++vt+ti+  ee +++ k++ ++ a l+ae+ +ri+++ sv slf
  lcl|FitnessBrowser__Burk376:H281DRAFT_01939 270 ELVVTDTIPLgEEaRSCAKIRSLTSAGLLAETFSRIRRGDSVMSLF 315
                                                  **********9888*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (318 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.47
//
[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