GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Magnetospirillum magneticum AMB-1

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 WP_009871053.1 AMB_RS03050 ribose-phosphate pyrophosphokinase

Query= SwissProt::P0A1V6
         (315 letters)



>NCBI__GCF_000009985.1:WP_009871053.1
          Length = 310

 Score =  335 bits (858), Expect = 1e-96
 Identities = 171/312 (54%), Positives = 235/312 (75%), Gaps = 3/312 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           MK+ A N+   LA+ IA  L  S+  A + RFSD EV V+I+ENVRG D+F+IQST  P 
Sbjct: 1   MKILACNSNRPLAEAIAEYLTMSITKAVIRRFSDNEVFVEIHENVRGEDVFVIQSTSYPA 60

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMEL+V +DALRR SA RITAVIPYFGYARQDR+  S R PI+AK+VA+ +++ G D
Sbjct: 61  NDNLMELLVTLDALRRGSARRITAVIPYFGYARQDRK-SSPRSPISAKLVANLITTAGAD 119

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDM-LQLNLDNPIVVSPDIGGVVRARAIAK 182
           RV+T+DLH+ QIQGFFD+P+DN++ +P+   D+  +   D+ +VVSPD+GGVVRARAIA 
Sbjct: 120 RVVTLDLHSGQIQGFFDIPLDNLYAAPVFTNDIRARYQGDDVMVVSPDVGGVVRARAIAS 179

Query: 183 LLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAK 242
            + D D+AIIDKRR +A VS+VM+IIGDV GR C++VDD++D+ GTLC AAEAL + GA 
Sbjct: 180 RI-DADLAIIDKRREKAGVSEVMNIIGDVRGRRCIMVDDIVDSAGTLCNAAEALMKAGAV 238

Query: 243 RVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLTDEIKALPNVRTLTLSGMLAEAIRR 302
            V A+ TH + SG A   +  S ++E+V+ D+IP T+ +K   N+R +T++ ++AE+I R
Sbjct: 239 SVAAFVTHGVLSGGAVARVTASPLEELVITDSIPATEAVKMARNIRQVTIAPLMAESISR 298

Query: 303 ISNEESISAMFE 314
           IS E S+S++F+
Sbjct: 299 ISEERSVSSLFD 310


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: 284
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: 310
Length adjustment: 27
Effective length of query: 288
Effective length of database: 283
Effective search space:    81504
Effective search space used:    81504
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 WP_009871053.1 AMB_RS03050 (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.19683.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-121  388.6   2.4   9.2e-121  388.4   2.4    1.0  1  lcl|NCBI__GCF_000009985.1:WP_009871053.1  AMB_RS03050 ribose-phosphate pyr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_009871053.1  AMB_RS03050 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.4   2.4  9.2e-121  9.2e-121       1     309 []       1     310 []       1     310 [] 0.98

  Alignments for each domain:
  == domain 1  score: 388.4 bits;  conditional E-value: 9.2e-121
                                 TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 
                                               +kil+++s++ lae++a++l ++++++ +++F+d+E+ v+i+e+vrg+dvf+i qsts p nd+lmell
  lcl|NCBI__GCF_000009985.1:WP_009871053.1   1 MKILACNSNRPLAEAIAEYLTMSITKAVIRRFSDNEVFVEIHENVRGEDVFVI-QSTSYPANDNLMELL 68 
                                               79***************************************************.99999********** PP

                                 TIGR01251  70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdv 138
                                               +++dal+r sa+++taviPy+gYaRqd+k ++r+pisaklva+l+++aGadrv+t+dlHs qiqgfFd+
  lcl|NCBI__GCF_000009985.1:WP_009871053.1  69 VTLDALRRGSARRITAVIPYFGYARQDRKSSPRSPISAKLVANLITTAGADRVVTLDLHSGQIQGFFDI 137
                                               ********************************************************************* PP

                                 TIGR01251 139 pvenlsaspklieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllg 206
                                               p++nl+a+p++++++++++  ++++vvsPD G+v ra+++a++++++laii+K+R+ k+ + ev+n++g
  lcl|NCBI__GCF_000009985.1:WP_009871053.1 138 PLDNLYAAPVFTNDIRARYqGDDVMVVSPDVGGVVRARAIASRIDADLAIIDKRRE-KAGVSEVMNIIG 205
                                               *****************998999*********************************.777********* PP

                                 TIGR01251 207 dvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv. 274
                                               dv g+ +++vDDi++++gTl++aae+L ++GA +v + +thgv+sg A+ r++ + +ee+++t++i+  
  lcl|NCBI__GCF_000009985.1:WP_009871053.1 206 DVRGRRCIMVDDIVDSAGTLCNAAEALMKAGAVSVAAFVTHGVLSGGAVARVTASPLEELVITDSIPAt 274
                                               ********************************************************************5 PP

                                 TIGR01251 275 ee.kklpkvseisvapliaeaiarihenesvsslfd 309
                                               e  k   +++++++apl+ae i+ri+e++svsslfd
  lcl|NCBI__GCF_000009985.1:WP_009871053.1 275 EAvKMARNIRQVTIAPLMAESISRISEERSVSSLFD 310
                                               559999****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (310 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: 6.96
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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