Alignments for a candidate for prs in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Mycolicibacterium vanbaalenii PYR-1

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_011781930.1 MVAN_RS24035 ribose-phosphate diphosphokinase

Query= BRENDA::A0R3C8
         (326 letters)



>NCBI__GCF_000015305.1:WP_011781930.1
          Length = 326

 Score =  601 bits (1549), Expect = e-177
 Identities = 301/326 (92%), Positives = 313/326 (96%)

Query: 1   MATDWTDNRKNLMLFAGRAHPELADQVAKELDVAVTAQTARDFANGEIFVRFDESVRGCD 60
           M+ DWTDNRKNLMLF+GRAHPELA+QVAKELDV VTAQTARDFANGEIFVRFDESVRGCD
Sbjct: 1   MSHDWTDNRKNLMLFSGRAHPELAEQVAKELDVPVTAQTARDFANGEIFVRFDESVRGCD 60

Query: 61  AFVLQSHPAPLNQWLMEQLIMIDALKRGSAKRITAILPFYPYARQDKKHRGREPISARLV 120
           AFVLQSHPAPLN WLMEQLIMIDALKRGSAKRITAILPFYPYARQDKKHRGREPISARLV
Sbjct: 61  AFVLQSHPAPLNTWLMEQLIMIDALKRGSAKRITAILPFYPYARQDKKHRGREPISARLV 120

Query: 121 ADLLKTAGADRIVSVDLHTDQIQGFFDGPVDHMRAQKLLTGYIGEHYADEDMVVVSPDSG 180
           ADL KTAGADRIV+VDLHTDQIQGFFDGPVDHMRAQKLLTGYI E+YAD DMVVVSPDSG
Sbjct: 121 ADLYKTAGADRIVTVDLHTDQIQGFFDGPVDHMRAQKLLTGYIAENYADHDMVVVSPDSG 180

Query: 181 RVRVAEKWADSLGGVPLAFIHKTRDPLVPNQVKSNRVVGDVKGKTCILTDDMIDTGGTIA 240
           RVRVAEKWAD+LGGVPLAFIHKTRDPLVPNQVKSNRVVGDVKG+TCILTDDMIDTGGTIA
Sbjct: 181 RVRVAEKWADALGGVPLAFIHKTRDPLVPNQVKSNRVVGDVKGRTCILTDDMIDTGGTIA 240

Query: 241 GAVNLLREDGAKDVIIAATHGVLSDPAPQRLAECGAREVIVTNTLPITEDKRFPQLTVLS 300
           GAV LL++DGA DV+IAATHGVLSDPA +RLAE GAREVIVTNTLPI EDK FPQLTVLS
Sbjct: 241 GAVRLLKQDGAADVVIAATHGVLSDPARERLAESGAREVIVTNTLPIGEDKMFPQLTVLS 300

Query: 301 IAPLLANTIRAVFENGSVTGLFDGSA 326
           IAPLLANTIRAVF+NGSVT LFDGSA
Sbjct: 301 IAPLLANTIRAVFDNGSVTSLFDGSA 326


Lambda     K      H
   0.320    0.136    0.400 

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: 488
Number of extensions: 13
Number of successful extensions: 1
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: 326
Length of database: 326
Length adjustment: 28
Effective length of query: 298
Effective length of database: 298
Effective search space:    88804
Effective search space used:    88804
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_011781930.1 MVAN_RS24035 (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.19737.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-124  398.7   0.0   7.8e-124  398.5   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011781930.1  MVAN_RS24035 ribose-phosphate di


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011781930.1  MVAN_RS24035 ribose-phosphate diphosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.5   0.0  7.8e-124  7.8e-124       2     309 .]      13     323 ..      12     323 .. 0.99

  Alignments for each domain:
  == domain 1  score: 398.5 bits;  conditional E-value: 7.8e-124
                                 TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmelll 70 
                                               +++sg++++elae+vak+l+++++ ++ + Fa+gE+ vr++esvrg+d f++ qs  ap n +lme l+
  lcl|NCBI__GCF_000015305.1:WP_011781930.1  13 MLFSGRAHPELAEQVAKELDVPVTAQTARDFANGEIFVRFDESVRGCDAFVL-QSHPAPLNTWLMEQLI 80 
                                               79**************************************************.**************** PP

                                 TIGR01251  71 lidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFdvp 139
                                               +idalkr sak++ta++P+y+YaRqdkk+++repisa+lva+l+++aGadr++tvdlH++qiqgfFd p
  lcl|NCBI__GCF_000015305.1:WP_011781930.1  81 MIDALKRGSAKRITAILPFYPYARQDKKHRGREPISARLVADLYKTAGADRIVTVDLHTDQIQGFFDGP 149
                                               ********************************************************************* PP

                                 TIGR01251 140 venlsaspklieelkkke.lknlvvvsPDkGaverakkvakklg.lelaiieKeRds.kenevevtnll 205
                                               v++++a++ l+ ++++++ ++++vvvsPD+G v+ a+k+a++lg ++la+i+K+Rd    n+v++++++
  lcl|NCBI__GCF_000015305.1:WP_011781930.1 150 VDHMRAQKLLTGYIAENYaDHDMVVVSPDSGRVRVAEKWADALGgVPLAFIHKTRDPlVPNQVKSNRVV 218
                                               *****************99*************************9***********98899******** PP

                                 TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                               gdv+g++++++DD+i+TggT++ a++lLk++GA +v++aathgv+s++A erlae+g++evivtnt+++
  lcl|NCBI__GCF_000015305.1:WP_011781930.1 219 GDVKGRTCILTDDMIDTGGTIAGAVRLLKQDGAADVVIAATHGVLSDPARERLAESGAREVIVTNTLPI 287
                                               ********************************************************************* PP

                                 TIGR01251 275 .eekklpkvseisvapliaeaiarihenesvsslfd 309
                                                e+k +p+++++s+apl+a++i+++ +n sv+slfd
  lcl|NCBI__GCF_000015305.1:WP_011781930.1 288 gEDKMFPQLTVLSIAPLLANTIRAVFDNGSVTSLFD 323
                                               999*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (326 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.85
//
[ok]

This GapMind analysis is from Apr 10 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