Alignments for a candidate for prs in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Steroidobacter denitrificans DSM 18526

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate WP_066918431.1 ACG33_RS02555 ribose-phosphate pyrophosphokinase

Query= BRENDA::P0A719
         (315 letters)



>NCBI__GCF_001579945.1:WP_066918431.1
          Length = 317

 Score =  394 bits (1011), Expect = e-114
 Identities = 193/310 (62%), Positives = 252/310 (81%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           M +FAG+A  +LA  IA  +   LG A+VGRFSDGE +V++ ENVRG DIFI+Q T  P 
Sbjct: 6   MAVFAGSANRQLAHDIARHMMVPLGRASVGRFSDGETTVELLENVRGRDIFIVQPTSPPA 65

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           N+++MEL+VMVDA RRASA RITAV+PYFGYARQDRR R+ RVPITAK+VA+ ++S GVD
Sbjct: 66  NEHVMELLVMVDACRRASAARITAVVPYFGYARQDRRPRATRVPITAKLVANMIASAGVD 125

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183
           RVLTVDLHA+QIQGFFD+PVDNV+ SP+LL D+ +   DN +VVSPD+GGVVRARA+AK 
Sbjct: 126 RVLTVDLHADQIQGFFDIPVDNVYASPVLLGDVWRRKYDNLMVVSPDVGGVVRARALAKR 185

Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243
           L+D ++AIIDKRRPRAN S+VM+IIG+VAG+ CVLVDD++DT GTLC AA+ALK+ GA++
Sbjct: 186 LDDAELAIIDKRRPRANESEVMNIIGEVAGKTCVLVDDLVDTAGTLCHAAQALKKAGAQK 245

Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303
           V+AY TH + SG A   +  S +DE+VV DTIPLS+  +    +R L+++G+LAE +RRI
Sbjct: 246 VYAYITHAVLSGPAIERITKSDLDELVVTDTIPLSEAARQCTKIRQLSVAGLLAETMRRI 305

Query: 304 SNEESISAMF 313
            +EES+S+++
Sbjct: 306 RDEESVSSLY 315


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: 299
Number of extensions: 10
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: 315
Length of database: 317
Length adjustment: 27
Effective length of query: 288
Effective length of database: 290
Effective search space:    83520
Effective search space used:    83520
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_066918431.1 ACG33_RS02555 (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.25110.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-123  398.1   0.4   1.2e-123  397.9   0.4    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066918431.1  ACG33_RS02555 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066918431.1  ACG33_RS02555 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.9   0.4  1.2e-123  1.2e-123       1     308 [.       6     315 ..       6     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 397.9 bits;  conditional E-value: 1.2e-123
                                 TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 
                                               + +++gs++++la+ +a+++ ++lg+++v +F+dgE+ v++ e+vrg+d+fi+ q ts+p n+++mell
  lcl|NCBI__GCF_001579945.1:WP_066918431.1   6 MAVFAGSANRQLAHDIARHMMVPLGRASVGRFSDGETTVELLENVRGRDIFIV-QPTSPPANEHVMELL 73 
                                               679**************************************************.*************** PP

                                 TIGR01251  70 llidalkrasaksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFd 137
                                               +++da++rasa ++tav+Py+gYaRqd++ +  r pi+aklva+++++aG+drvltvdlH++qiqgfFd
  lcl|NCBI__GCF_001579945.1:WP_066918431.1  74 VMVDACRRASAARITAVVPYFGYARQDRRPRaTRVPITAKLVANMIASAGVDRVLTVDLHADQIQGFFD 142
                                               ****************************98758************************************ PP

                                 TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnll 205
                                               +pv+n++asp+l+ ++ +++ +nl+vvsPD G+v ra+++ak+l+ +elaii+K+R+ ++ne ev+n++
  lcl|NCBI__GCF_001579945.1:WP_066918431.1 143 IPVDNVYASPVLLGDVWRRKYDNLMVVSPDVGGVVRARALAKRLDdAELAIIDKRRP-RANESEVMNII 210
                                               *********************************************9***********.889******** PP

                                 TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                               g+v+gk++v+vDD+++T+gTl++aa++Lk++GA+kv++++th+v+sg+A+er++++ ++e++vt+ti+ 
  lcl|NCBI__GCF_001579945.1:WP_066918431.1 211 GEVAGKTCVLVDDLVDTAGTLCHAAQALKKAGAQKVYAYITHAVLSGPAIERITKSDLDELVVTDTIPL 279
                                               ********************************************************************* PP

                                 TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslf 308
                                                e  +++ k++++sva l+ae+++ri+++esvssl+
  lcl|NCBI__GCF_001579945.1:WP_066918431.1 280 sEAaRQCTKIRQLSVAGLLAETMRRIRDEESVSSLY 315
                                               65589*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (317 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: 00:00:00.01
# Mc/sec: 7.39
//
[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