Alignments for a candidate for prs in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Pedobacter sp. GW460-11-11-14-LB5

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate CA265_RS24735 CA265_RS24735 ribose-phosphate pyrophosphokinase

Query= BRENDA::E7EAU9
         (317 letters)



>FitnessBrowser__Pedo557:CA265_RS24735
          Length = 313

 Score =  290 bits (743), Expect = 2e-83
 Identities = 158/307 (51%), Positives = 210/307 (68%), Gaps = 3/307 (0%)

Query: 10  LKIFSLNSNPELAKEIADNVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSAPV 69
           +K+FS   +  L+ +IA++ G  LG  ++ +FSDGE Q + +ESIRG D ++IQST  P 
Sbjct: 8   VKLFSGTGSRGLSLKIAEHYGKPLGSVTIHKFSDGEFQPSFDESIRGSDVFLIQSTYQP- 66

Query: 70  NEHIMELLIMVDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLFANLLETAGATR 129
           ++++MELL+MVDA KRASA  I  V+PYYG ARQDRK + R  I AKL ANLL++AG  R
Sbjct: 67  SDNLMELLLMVDAAKRASAHYITAVVPYYGLARQDRKDKPRVAIGAKLVANLLKSAGIHR 126

Query: 130 VIALDLHAPQIQGFFDIPIDHLMGVPILGHYFEGKDLKDIVIVSPDHGGVTRARKLADRL 189
           ++ +DLHA QIQGFFDIP+DHL G  I   Y +   LK++ I SPD GG  RAR  A   
Sbjct: 127 IMTMDLHAAQIQGFFDIPVDHLDGSVIFVPYIKSLGLKNLTIASPDMGGSYRARTFAKFF 186

Query: 190 KAPIAIIDKRRPRPNEVEVMNIVGNVEGKTAILIDDIIDTAGTITLAANALVENGAAEVY 249
            A + I DKRR R NE+E M+I+G+V G+  +LIDDI DTAGT++ AA  ++ENGAA V 
Sbjct: 187 NAEVIICDKRRKRANEIESMSIIGDVTGQDVVLIDDICDTAGTLSKAAALIMENGAASVR 246

Query: 250 ACCTHPVLSGPAVERINNSKIKELVVTNSIKLPEEKKIERFKQLSVGPLLAEAIIRVHEK 309
           A CTH VLSG A+E + NS + EL+VT++I L +E    + + LS   L A AI  V+E 
Sbjct: 247 AVCTHAVLSGKAIETVENSVLTELIVTDTIPLKQES--PKIRVLSTAGLFARAIANVNEH 304

Query: 310 QSVSYLF 316
            S+S LF
Sbjct: 305 GSISDLF 311


Lambda     K      H
   0.319    0.136    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: 203
Number of extensions: 5
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: 313
Length adjustment: 27
Effective length of query: 290
Effective length of database: 286
Effective search space:    82940
Effective search space used:    82940
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 CA265_RS24735 CA265_RS24735 (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.12226.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.2e-110  352.7   0.1     8e-110  352.5   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS24735  CA265_RS24735 ribose-phosphate p


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS24735  CA265_RS24735 ribose-phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.5   0.1    8e-110    8e-110       2     309 .]       9     312 ..       8     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 352.5 bits;  conditional E-value: 8e-110
                                  TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmell 69 
                                                k++sg+ s+ l+ k+a++ g +lg+v+++kF+dgE++  ++es+rg+dvf+i qst++  +d+lmell
  lcl|FitnessBrowser__Pedo557:CA265_RS24735   9 KLFSGTGSRGLSLKIAEHYGKPLGSVTIHKFSDGEFQPSFDESIRGSDVFLI-QSTYQ-PSDNLMELL 74 
                                                79**************************************************.99995.799****** PP

                                  TIGR01251  70 llidalkrasaksvtaviPyygYaRqdkkaksrepisaklvaklleeaGadrvltvdlHseqiqgfFd 137
                                                l++da+krasa+ +tav+Pyyg aRqd+k+k+r +i aklva+ll++aG++r++t+dlH+ qiqgfFd
  lcl|FitnessBrowser__Pedo557:CA265_RS24735  75 LMVDAAKRASAHYITAVVPYYGLARQDRKDKPRVAIGAKLVANLLKSAGIHRIMTMDLHAAQIQGFFD 142
                                                ******************************************************************** PP

                                  TIGR01251 138 vpvenlsaspklieelkkkelknlvvvsPDkGaverakkvakklglelaiieKeRdskenevevtnll 205
                                                +pv++l++s  ++ ++k+  lknl++ sPD G+  ra+++ak  ++e+ i +K+R+ ++ne+e++ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS24735 143 IPVDHLDGSVIFVPYIKSLGLKNLTIASPDMGGSYRARTFAKFFNAEVIICDKRRK-RANEIESMSII 209
                                                ******************99************************************.889******** PP

                                  TIGR01251 206 gdvegkdvvivDDiisTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntil 273
                                                gdv g+dvv++DDi +T+gTl kaa l+ e+GA +v +++th+v+sg+A+e +++++++e+ivt+ti+
  lcl|FitnessBrowser__Pedo557:CA265_RS24735 210 GDVTGQDVVLIDDICDTAGTLSKAAALIMENGAASVRAVCTHAVLSGKAIETVENSVLTELIVTDTIP 277
                                                ******************************************************************** PP

                                  TIGR01251 274 veekklpkvseisvapliaeaiarihenesvsslfd 309
                                                  +++ pk++++s a l+a+aia+++e+ s+s lf+
  lcl|FitnessBrowser__Pedo557:CA265_RS24735 278 L-KQESPKIRVLSTAGLFARAIANVNEHGSISDLFR 312
                                                *.8899****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (313 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: 00:00:00.00
# Mc/sec: 10.03
//
[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