Alignments for a candidate for prs in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Echinicola vietnamensis KMM 6221, DSM 17526

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate Echvi_4597 Echvi_4597 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__Cola:Echvi_4597
          Length = 309

 Score =  295 bits (754), Expect = 1e-84
 Identities = 158/314 (50%), Positives = 215/314 (68%), Gaps = 7/314 (2%)

Query: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60
           MP++KLFAG  T +LA  IA      LG   +  FSDGE+S   +E+VRG  +F+IQST 
Sbjct: 1   MPEVKLFAGTNTKKLADSIAGNYGQDLGAMTLSMFSDGEMSPSFDESVRGCHVFLIQST- 59

Query: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120
            P  DNL+EL +M+DA +RASA ++ AV+PY+GYARQDR+ R  RV I AK++A+ + S 
Sbjct: 60  NPNADNLLELCLMIDAAKRASAYKVCAVVPYYGYARQDRKDRP-RVSIAAKLIANMIMSA 118

Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNL-DNPIVVSPDIGGVVRARA 179
           G DR++T DLHA QIQGFFD+P+D++ GS I +  +  L+L DN I  SPD+GGV RARA
Sbjct: 119 GADRIMTCDLHAGQIQGFFDIPLDHLNGSAIFVPYLKSLDLGDNLIFASPDVGGVSRARA 178

Query: 180 IAKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKER 239
            AK   + DM + DK R RAN    M +IGDV G+D VLVDD++DT GT+CKAAE L ++
Sbjct: 179 YAKHF-EVDMVVCDKHRKRANEVASMQVIGDVEGKDVVLVDDLVDTAGTMCKAAEILLDK 237

Query: 240 GAKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEA 299
           GA  V A ATH + SG A  N+ NS + E+V+ DTIP+    K    ++ LT++ + A+A
Sbjct: 238 GANSVRAIATHGVLSGKAYENIENSKLSELVITDTIPIK---KESSKIKVLTVAELFAKA 294

Query: 300 IRRISNEESISAMF 313
           I  ++  +SISA+F
Sbjct: 295 IHAVTGNDSISALF 308


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: 280
Number of extensions: 13
Number of successful extensions: 6
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: 309
Length adjustment: 27
Effective length of query: 288
Effective length of database: 282
Effective search space:    81216
Effective search space used:    81216
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 Echvi_4597 Echvi_4597 (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.3545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   3.4e-110  353.7   0.5   3.8e-110  353.6   0.5    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4597  Echvi_4597 ribose-phosphate pyro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4597  Echvi_4597 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.6   0.5  3.8e-110  3.8e-110       2     308 ..       5     308 ..       4     309 .] 0.98

  Alignments for each domain:
  == domain 1  score: 353.6 bits;  conditional E-value: 3.8e-110
                            TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidal 75 
                                          k+++g+++k+la+++a n g++lg ++   F+dgE++  ++esvrg++vf+i qst  p  d+l+el l+ida+
  lcl|FitnessBrowser__Cola:Echvi_4597   5 KLFAGTNTKKLADSIAGNYGQDLGAMTLSMFSDGEMSPSFDESVRGCHVFLI-QSTN-PNADNLLELCLMIDAA 76 
                                          799*************************************************.7777.789************* PP

                            TIGR01251  76 krasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspkl 149
                                          krasa +v av+PyygYaRqd+k+++r +i+akl+a+++ +aGadr++t dlH+ qiqgfFd+p+++l++s  +
  lcl|FitnessBrowser__Cola:Echvi_4597  77 KRASAYKVCAVVPYYGYARQDRKDRPRVSIAAKLIANMIMSAGADRIMTCDLHAGQIQGFFDIPLDHLNGSAIF 150
                                          ************************************************************************** PP

                            TIGR01251 150 ieelkkke.lknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDiisT 222
                                          + +lk+    +nl++ sPD G+v+ra+++ak+ ++++++ +K+R+ ++nev +++++gdvegkdvv+vDD+++T
  lcl|FitnessBrowser__Cola:Echvi_4597 151 VPYLKSLDlGDNLIFASPDVGGVSRARAYAKHFEVDMVVCDKHRK-RANEVASMQVIGDVEGKDVVLVDDLVDT 223
                                          ******99899**********************************.889************************* PP

                            TIGR01251 223 ggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilveekklpkvseisvapliaeaia 296
                                          +gT++kaae+L +kGA++v ++athgv+sg+A+e+++++ ++e+++t+ti++ +k+ +k+++++va+l+a+ai 
  lcl|FitnessBrowser__Cola:Echvi_4597 224 AGTMCKAAEILLDKGANSVRAIATHGVLSGKAYENIENSKLSELVITDTIPI-KKESSKIKVLTVAELFAKAIH 296
                                          ****************************************************.8899***************** PP

                            TIGR01251 297 rihenesvsslf 308
                                          +++ n s+s+lf
  lcl|FitnessBrowser__Cola:Echvi_4597 297 AVTGNDSISALF 308
                                          ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (309 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.70
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis