GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Sphingomonas koreensis DSMZ 15582

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate Ga0059261_2274 Ga0059261_2274 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__Korea:Ga0059261_2274
          Length = 311

 Score =  331 bits (848), Expect = 2e-95
 Identities = 171/312 (54%), Positives = 231/312 (74%), Gaps = 2/312 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           MKL AGN+   LAQ IA+ L   L  A V RF+D E+ V+I ENVRG D+F++QST  P 
Sbjct: 1   MKLMAGNSNLPLAQAIASYLEIPLTQANVRRFADEEIFVEILENVRGEDVFVLQSTAYPA 60

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMEL++M+DALRRASA RITAV+PYFGYARQDR+    R PI+AK+VA+ +++ G +
Sbjct: 61  NDNLMELLIMIDALRRASAKRITAVLPYFGYARQDRKP-GPRTPISAKLVANLITTAGAN 119

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLD-NPIVVSPDIGGVVRARAIAK 182
           RVL+VDLHA QIQGFFD+P DN+F +P++ ED+     D N +VVSPD+GGVVRARA+AK
Sbjct: 120 RVLSVDLHAGQIQGFFDIPTDNLFAAPVMSEDIKARFSDKNLMVVSPDVGGVVRARALAK 179

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            L +  +AI+DKRR +A  S+VM+IIGDV GR C+L+DD++D+ GTLC AA ALK  GA+
Sbjct: 180 RLENAPLAIVDKRREKAGESEVMNIIGDVEGRFCILIDDIVDSAGTLCNAAAALKAAGAE 239

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRR 302
            V AY TH + SG A   +  S + E+V+ D+I     +     +R LT++ ++AEAIRR
Sbjct: 240 GVVAYCTHGVLSGGAVARVDGSELSELVITDSIGNHAIVGEAQRIRHLTIAPLIAEAIRR 299

Query: 303 ISNEESISAMFE 314
           I++E S+S++F+
Sbjct: 300 IADESSVSSLFD 311


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: 301
Number of extensions: 10
Number of successful extensions: 3
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: 311
Length adjustment: 27
Effective length of query: 288
Effective length of database: 284
Effective search space:    81792
Effective search space used:    81792
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 Ga0059261_2274 Ga0059261_2274 (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.3905891.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-118  378.8   0.1   8.9e-118  378.6   0.1    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2274  Ga0059261_2274 ribose-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2274  Ga0059261_2274 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.6   0.1  8.9e-118  8.9e-118       1     309 []       1     311 []       1     311 [] 0.98

  Alignments for each domain:
  == domain 1  score: 378.6 bits;  conditional E-value: 8.9e-118
                                 TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 
                                               +k+++g+s+  la+++a +l+++l++++v++Fad+E+ v+i e+vrg+dvf++ qst  p nd+lmell
  lcl|FitnessBrowser__Korea:Ga0059261_2274   1 MKLMAGNSNLPLAQAIASYLEIPLTQANVRRFADEEIFVEILENVRGEDVFVL-QSTAYPANDNLMELL 68 
                                               7899*************************************************.99999********** PP

                                 TIGR01251  70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138
                                               ++idal+rasak++tav+Py+gYaRqd+k  +r+pisaklva+l+++aGa+rvl vdlH+ qiqgfFd+
  lcl|FitnessBrowser__Korea:Ga0059261_2274  69 IMIDALRRASAKRITAVLPYFGYARQDRKPGPRTPISAKLVANLITTAGANRVLSVDLHAGQIQGFFDI 137
                                               ********************************************************************* PP

                                 TIGR01251 139 pvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnll 205
                                               p +nl a+p++ e++k++  +knl+vvsPD G+v ra+++ak+l+ ++lai++K+R+ k+ e ev+n++
  lcl|FitnessBrowser__Korea:Ga0059261_2274 138 PTDNLFAAPVMSEDIKARFsDKNLMVVSPDVGGVVRARALAKRLEnAPLAIVDKRRE-KAGESEVMNII 205
                                               *****************999************************99***********.777******** PP

                                 TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                               gdveg+ ++++DDi++++gTl++aa +Lk +GA+ v++++thgv+sg A+ r++ + ++e+++t++i  
  lcl|FitnessBrowser__Korea:Ga0059261_2274 206 GDVEGRFCILIDDIVDSAGTLCNAAAALKAAGAEGVVAYCTHGVLSGGAVARVDGSELSELVITDSIGN 274
                                               *******************************************************************99 PP

                                 TIGR01251 275 ee..kklpkvseisvapliaeaiarihenesvsslfd 309
                                               +    + ++++++++apliaeai+ri++++svsslfd
  lcl|FitnessBrowser__Korea:Ga0059261_2274 275 HAivGEAQRIRHLTIAPLIAEAIRRIADESSVSSLFD 311
                                               5558999****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (311 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 19.71
//
[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