GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Caldicellulosiruptor kronotskyensis 2002

Align Ribose-phosphate pyrophosphokinase; RPPK; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PPRibP synthase; PRPP synthase; PRPPase; EC 2.7.6.1 (characterized)
to candidate WP_013403879.1 CALKRO_RS10070 ribose-phosphate diphosphokinase

Query= SwissProt::P14193
         (317 letters)



>NCBI__GCF_000166775.1:WP_013403879.1
          Length = 325

 Score =  406 bits (1043), Expect = e-118
 Identities = 200/310 (64%), Positives = 250/310 (80%), Gaps = 1/310 (0%)

Query: 8   KNLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSD 67
           K +KIF+ NSN ELA+EIA  +G +LG   + RFSDGE+ + I E++RG D +++QST  
Sbjct: 6   KEIKIFTGNSNKELAEEIASHLGKKLGDAEIGRFSDGEISVRINETVRGADVFVVQSTCH 65

Query: 68  PVNEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGA 127
           PVNE++MELLIM+DA KRASA  I  VIPYYGYARQDRKAR+R+PITAKL ANL+ +AGA
Sbjct: 66  PVNENLMELLIMIDAFKRASAGRITAVIPYYGYARQDRKARARDPITAKLVANLITSAGA 125

Query: 128 TRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYF-EGKNLEDIVIVSPDHGGVTRARKLA 186
            RV+ +DLHAPQIQGFFDIP+DHL+GVPIL +YF E  NLE+ V+VSPD G VTRAR  A
Sbjct: 126 DRVLTMDLHAPQIQGFFDIPLDHLIGVPILAKYFMENVNLENAVVVSPDLGSVTRARNFA 185

Query: 187 DRLKAPIAIIDKRRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAK 246
            +L  P+AI+DKRRP+ NVAE+MNI+G+++ KT +++DD+IDTAGTI  AA AL++ GAK
Sbjct: 186 TKLDLPLAIVDKRRPKANVAEIMNIIGDVKDKTCLMVDDMIDTAGTIVAAAQALMDYGAK 245

Query: 247 EVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRV 306
           EVYACCTHPVLSGPAVERI  S IKELVV N+I LP EK+I++ K LSV  L AEAI R+
Sbjct: 246 EVYACCTHPVLSGPAVERIQQSPIKELVVLNTIPLPPEKRIDKIKVLSVASLFAEAITRI 305

Query: 307 HEQQSVSYLF 316
           +E  ++S LF
Sbjct: 306 YEDVAISTLF 315


Lambda     K      H
   0.319    0.137    0.383 

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: 305
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: 317
Length of database: 325
Length adjustment: 28
Effective length of query: 289
Effective length of database: 297
Effective search space:    85833
Effective search space used:    85833
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_013403879.1 CALKRO_RS10070 (ribose-phosphate diphosphokinase)
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.2018066.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-133  429.9   0.7   2.4e-133  429.7   0.7    1.0  1  NCBI__GCF_000166775.1:WP_013403879.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013403879.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.7   0.7  2.4e-133  2.4e-133       1     309 []       8     316 ..       8     316 .. 0.99

  Alignments for each domain:
  == domain 1  score: 429.7 bits;  conditional E-value: 2.4e-133
                             TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllid 73 
                                           +ki+ g+s+kelae++a +lg +lgd+e+ +F+dgE++vri+e+vrg dvf++ qst++pvn++lmell++id
  NCBI__GCF_000166775.1:WP_013403879.1   8 IKIFTGNSNKELAEEIASHLGKKLGDAEIGRFSDGEISVRINETVRGADVFVV-QSTCHPVNENLMELLIMID 79 
                                           589**************************************************.9****************** PP

                             TIGR01251  74 alkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsas 146
                                           a+krasa+++taviPyygYaRqd+ka+ r+pi+aklva+l+++aGadrvlt+dlH++qiqgfFd+p+++l + 
  NCBI__GCF_000166775.1:WP_013403879.1  80 AFKRASAGRITAVIPYYGYARQDRKARARDPITAKLVANLITSAGADRVLTMDLHAPQIQGFFDIPLDHLIGV 152
                                           ************************************************************************* PP

                             TIGR01251 147 pklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDD 218
                                           p l++++ +++ l+n vvvsPD G+v+ra+++a+kl+l+lai++K+R+ k+n++e++n++gdv++k++++vDD
  NCBI__GCF_000166775.1:WP_013403879.1 153 PILAKYFMENVnLENAVVVSPDLGSVTRARNFATKLDLPLAIVDKRRP-KANVAEIMNIIGDVKDKTCLMVDD 224
                                           *********999************************************.899********************* PP

                             TIGR01251 219 iisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv.eekklpkvseisvapl 290
                                           +i+T+gT+v+aa++L + GAk+v++++th+v+sg+A+er++++ ++e++v nti+   ek+++k++++sva l
  NCBI__GCF_000166775.1:WP_013403879.1 225 MIDTAGTIVAAAQALMDYGAKEVYACCTHPVLSGPAVERIQQSPIKELVVLNTIPLpPEKRIDKIKVLSVASL 297
                                           ********************************************************999************** PP

                             TIGR01251 291 iaeaiarihenesvsslfd 309
                                           +aeai+ri+e+ ++s+lfd
  NCBI__GCF_000166775.1:WP_013403879.1 298 FAEAITRIYEDVAISTLFD 316
                                           *****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (325 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: 22.44
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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