GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Pseudomonas fluorescens GW456-L13

Align ribose-phosphate diphosphokinase (EC 2.7.6.1) (characterized)
to candidate PfGW456L13_1577 Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)

Query= BRENDA::P0A719
         (315 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577
          Length = 313

 Score =  424 bits (1091), Expect = e-123
 Identities = 209/310 (67%), Positives = 257/310 (82%), Gaps = 1/310 (0%)

Query: 4   MKLFAGNATPELAQRIANRLYTSLGDAAVGRFSDGEVSVQINENVRGGDIFIIQSTCAPT 63
           M +F GNA P+LA+R+  +L+  LGD +VG+FSDGE++ +INENVRG D+FIIQ TCAPT
Sbjct: 4   MMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFIIQPTCAPT 63

Query: 64  NDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVD 123
           NDNLMELVVM DA RR+SA RITAVIPYFGYARQDRR RSARV I+AKVVAD L+ VG+D
Sbjct: 64  NDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRSARVAISAKVVADMLTVVGID 123

Query: 124 RVLTVDLHAEQIQGFFDVPVDNVFGSPILLEDMLQLNLDNPIVVSPDIGGVVRARAIAKL 183
           RVLTVDLHA+QIQGFFD+PVDN++GSP+L++D+     +N ++VSPDIGGVVRARA+AK 
Sbjct: 124 RVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIVSPDIGGVVRARAVAKS 183

Query: 184 LNDTDMAIIDKRRPRANVSQVMHIIGDVAGRDCVLVDDMIDTGGTLCKAAEALKERGAKR 243
           L   D+ IIDKRR +AN S+VMHIIGDV GR C+LVDDM+DT GTLC AA+ALKE GA +
Sbjct: 184 LG-VDLGIIDKRREKANHSEVMHIIGDVEGRTCILVDDMVDTAGTLCHAAKALKEHGAAK 242

Query: 244 VFAYATHPIFSGNAANNLRNSVIDEVVVCDTIPLSDEIKSLPNVRTLTLSGMLAEAIRRI 303
           VFAY THP+ SG A  N+ NSV+DE+VV +TIPLS   ++   +R L ++ ++AEA+RRI
Sbjct: 243 VFAYCTHPVLSGRAIENIENSVLDELVVTNTIPLSAAAQACARIRQLDIAPVVAEAVRRI 302

Query: 304 SNEESISAMF 313
           SNEESISAMF
Sbjct: 303 SNEESISAMF 312


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: 359
Number of extensions: 11
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: 315
Length of database: 313
Length adjustment: 27
Effective length of query: 288
Effective length of database: 286
Effective search space:    82368
Effective search space used:    82368
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 PfGW456L13_1577 (Ribose-phosphate pyrophosphokinase (EC 2.7.6.1))
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.17218.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   9.5e-127  408.1   2.8   1.1e-126  407.9   2.8    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  Ribose-phosphate pyrophosphokina


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  Ribose-phosphate pyrophosphokinase (EC 2.7.6.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   2.8  1.1e-126  1.1e-126       1     309 []       4     313 .]       4     313 .] 0.98

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 1.1e-126
                                               TIGR01251   1 lkilsgssskelaekvaknlglelgdvevkkFadgElyvrieesvrgkdvfiivq 55 
                                                             ++++ g+++++la++v ++l+++lgd++v kF+dgE+  +i+e+vrgkdvfii q
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577   4 MMVFTGNANPDLARRVVRQLHIPLGDISVGKFSDGEITAEINENVRGKDVFII-Q 57 
                                                             799**************************************************.* PP

                                               TIGR01251  56 stsapvndalmellllidalkrasaksvtaviPyygYaRqdkkak.srepisakl 109
                                                              t+ap+nd+lmel++++da++r+sa ++taviPy+gYaRqd++ +  r +isak+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577  58 PTCAPTNDNLMELVVMADAFRRSSATRITAVIPYFGYARQDRRPRsARVAISAKV 112
                                                             ******************************************97758******** PP

                                               TIGR01251 110 vaklleeaGadrvltvdlHseqiqgfFdvpvenlsaspklieelkkkelknlvvv 164
                                                             va++l+ +G+drvltvdlH++qiqgfFd+pv+n+++sp+l+++++++  +nl++v
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 113 VADMLTVVGIDRVLTVDLHADQIQGFFDIPVDNIYGSPVLVDDIEDQRFENLMIV 167
                                                             ******************************************************* PP

                                               TIGR01251 165 sPDkGaverakkvakklglelaiieKeRdskenevevtnllgdvegkdvvivDDi 219
                                                             sPD G+v ra++vak+lg++l ii+K+R+ k+n+ ev++++gdveg+++++vDD+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 168 SPDIGGVVRARAVAKSLGVDLGIIDKRRE-KANHSEVMHIIGDVEGRTCILVDDM 221
                                                             *****************************.899********************** PP

                                               TIGR01251 220 isTggTlvkaaelLkekGAkkvivaathgvfsgdAlerlaeagveevivtntilv 274
                                                             ++T+gTl++aa++Lke+GA kv++++th+v+sg+A+e++++++++e++vtnti+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 222 VDTAGTLCHAAKALKEHGAAKVFAYCTHPVLSGRAIENIENSVLDELVVTNTIPL 276
                                                             ******************************************************* PP

                                               TIGR01251 275 .ee.kklpkvseisvapliaeaiarihenesvsslfd 309
                                                                 +++ +++++++ap++aea++ri+++es+s++f+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1577 277 sAAaQACARIRQLDIAPVVAEAVRRISNEESISAMFR 313
                                                             65579******************************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: 00:00:00.01
# Mc/sec: 7.39
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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