Alignments for a candidate for prs in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prs in Shewanella oneidensis MR-1

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate 202924 SO3837 ribose-phosphate pyrophosphokinase (NCBI ptt file)

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__MR1:202924
          Length = 315

 Score =  529 bits (1362), Expect = e-155
 Identities = 263/315 (83%), Positives = 290/315 (92%)

Query: 1   MPDMKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTC 60
           MPD+KLFAGNATP LA++IA+RL+  LGDA VGRFSDGE+SVQINENVRG D+FIIQSTC
Sbjct: 1   MPDIKLFAGNATPSLAKKIADRLFCKLGDAVVGRFSDGEISVQINENVRGADVFIIQSTC 60

Query: 61  APTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120
           APTNDNLMEL+VMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV
Sbjct: 61  APTNDNLMELIVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSV 120

Query: 121 GVDRVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAI 180
           GVDRVLT DLHAEQIQGFFDVPVDNVFGSP+LLEDML   LDNP+VVSPDIGGVVRARA+
Sbjct: 121 GVDRVLTCDLHAEQIQGFFDVPVDNVFGSPVLLEDMLAKKLDNPVVVSPDIGGVVRARAV 180

Query: 181 AKLLNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERG 240
           AKLL+D+D+AIIDKRRP+ANV+QVMHIIGDV GRDC++VDDMIDTGGTLCKAAEALKE G
Sbjct: 181 AKLLDDSDLAIIDKRRPQANVAQVMHIIGDVQGRDCIIVDDMIDTGGTLCKAAEALKEHG 240

Query: 241 AKRVFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAI 300
           A RVFAYATHP+FSG AA N+ NSVIDEV+V DT+PLS E+  +  V  LT+S +LAEAI
Sbjct: 241 ANRVFAYATHPVFSGKAAENITNSVIDEVIVTDTVPLSPEMLKVAKVTQLTMSAVLAEAI 300

Query: 301 RRISNEESISAMFEH 315
           RR+SNEESISAMF H
Sbjct: 301 RRVSNEESISAMFSH 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: 425
Number of extensions: 6
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: 315
Length adjustment: 27
Effective length of query: 288
Effective length of database: 288
Effective search space:    82944
Effective search space used:    82944
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 202924 SO3837 (ribose-phosphate pyrophosphokinase (NCBI ptt file))
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.1409.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     3e-129  416.3   2.9   3.4e-129  416.1   2.9    1.0  1  lcl|FitnessBrowser__MR1:202924  SO3837 ribose-phosphate pyrophos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202924  SO3837 ribose-phosphate pyrophosphokinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.1   2.9  3.4e-129  3.4e-129       2     309 .]       5     314 ..       4     314 .. 0.98

  Alignments for each domain:
  == domain 1  score: 416.1 bits;  conditional E-value: 3.4e-129
                       TIGR01251   2 kilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivqstsapvndalmellllidalkrasa 80 
                                     k+++g+++++la+k+a++l  +lgd+ v +F+dgE++v+i+e+vrg dvfii qst+ap+nd+lmel++++dal+rasa
  lcl|FitnessBrowser__MR1:202924   5 KLFAGNATPSLAKKIADRLFCKLGDAVVGRFSDGEISVQINENVRGADVFII-QSTCAPTNDNLMELIVMVDALRRASA 82 
                                     89**************************************************.************************** PP

                       TIGR01251  81 ksvtaviPyygYaRqdkkak.srepisaklvaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkel 158
                                     +++taviPy+gYaRqd++++  r pi+ak+va++l+++G+drvlt dlH+eqiqgfFdvpv+n+ +sp+l+e++ +k+l
  lcl|FitnessBrowser__MR1:202924  83 GRITAVIPYFGYARQDRRVRsARVPITAKVVADFLSSVGVDRVLTCDLHAEQIQGFFDVPVDNVFGSPVLLEDMLAKKL 161
                                     ******************9857********************************************************* PP

                       TIGR01251 159 knlvvvsPDkGaverakkvakklg.lelaiieKeRdskenevevtnllgdvegkdvvivDDiisTggTlvkaaelLkek 236
                                     +n+vvvsPD G+v ra++vak l+ ++laii+K+R+ ++n+++v++++gdv+g+d++ivDD+i+TggTl+kaae+Lke+
  lcl|FitnessBrowser__MR1:202924 162 DNPVVVSPDIGGVVRARAVAKLLDdSDLAIIDKRRP-QANVAQVMHIIGDVQGRDCIIVDDMIDTGGTLCKAAEALKEH 239
                                     ***********************99***********.888*************************************** PP

                       TIGR01251 237 GAkkvivaathgvfsgdAlerlaeagveevivtntilv.ee.kklpkvseisvapliaeaiarihenesvsslfd 309
                                     GA++v+++ath+vfsg+A+e++++++++evivt+t++   e  k+ kv++++++ ++aeai+r++++es+s++f+
  lcl|FitnessBrowser__MR1:202924 240 GANRVFAYATHPVFSGKAAENITNSVIDEVIVTDTVPLsPEmLKVAKVTQLTMSAVLAEAIRRVSNEESISAMFS 314
                                     **************************************866699*****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (315 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: 6.31
//
[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