GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Pseudomonas putida KT2440

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate PP_2324 PP_2324 tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::P00888
         (356 letters)



>FitnessBrowser__Putida:PP_2324
          Length = 370

 Score =  417 bits (1072), Expect = e-121
 Identities = 205/350 (58%), Positives = 261/350 (74%), Gaps = 1/350 (0%)

Query: 6   LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65
           ++++++   + L+TP+QLK   PLS +    +   R+ + +I+ G+D RL VV GPCSIH
Sbjct: 18  IDDLNVASNETLITPDQLKKEIPLSAKALQTVTAGREVVRNILDGKDHRLFVVVGPCSIH 77

Query: 66  DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125
           D + A EYA R K LA EVSD+LYLVMRVYFEKPRTTVGWKGLINDP++D SF ++ GL 
Sbjct: 78  DIKAAHEYAERLKVLAEEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLH 137

Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185
           I RKLLL+L  MGLP ATEALDP SPQYL DL SWSAIGARTTESQTHREMASGLS  VG
Sbjct: 138 IGRKLLLDLAEMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVG 197

Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244
           FKNGTDG L  AINA+++ ++PHRF+GINQ G V+++ T+GNP GHV+LRGG   PNY  
Sbjct: 198 FKNGTDGGLTVAINALQSVSKPHRFLGINQEGGVSIVTTKGNPYGHVVLRGGNGKPNYDS 257

Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304
             VA CE+++ +A ++ ++MVDCSH NSNKD   QP V E+V  QI +GN+SIIGLM+ES
Sbjct: 258 VSVALCEQDLAKAKIKANIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVES 317

Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354
           +++ G QS  +   +++YGVS+TDACI W  T+  LR +H  L   L  R
Sbjct: 318 HLNWGCQSIPKNLDDLQYGVSITDACIDWSATEKTLRSMHAKLKDVLPQR 367


Lambda     K      H
   0.316    0.131    0.378 

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: 404
Number of extensions: 8
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: 356
Length of database: 370
Length adjustment: 29
Effective length of query: 327
Effective length of database: 341
Effective search space:   111507
Effective search space used:   111507
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate PP_2324 PP_2324 (tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.7913.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-155  503.1   0.0   1.7e-155  502.9   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_2324  PP_2324 tyr-sensitive phospho-2-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2324  PP_2324 tyr-sensitive phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.9   0.0  1.7e-155  1.7e-155       1     339 [.      19     361 ..      19     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: 502.9 bits;  conditional E-value: 1.7e-155
                           TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkla 75 
                                         ddl++++ + l+tP++lk+++pl++ka ++v+  r+ + +il+Gkd+rl+vv+GPcsihd +aa eya+rlk la
  lcl|FitnessBrowser__Putida:PP_2324  19 DDLNVASNETLITPDQLKKEIPLSAKALQTVTAGREVVRNILDGKDHRLFVVVGPCSIHDIKAAHEYAERLKVLA 93 
                                         78999999******************************************************************* PP

                           TIGR00034  76 eklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqylad 150
                                         e+++d l++vmrvyfekPrttvGWkGlindP+l++sf++++Gl+i rkllldl+e+glp+ate+ld+ispqyl d
  lcl|FitnessBrowser__Putida:PP_2324  94 EEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLHIGRKLLLDLAEMGLPTATEALDPISPQYLQD 168
                                         *************************************************************************** PP

                           TIGR00034 151 llswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedgh 225
                                         l+sw+aiGarttesq+hre+asgls +vgfkngtdG+l vai+a+++ +++h+fl+++++G v+iv+tkGn++gh
  lcl|FitnessBrowser__Putida:PP_2324 169 LISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGGLTVAINALQSVSKPHRFLGINQEGGVSIVTTKGNPYGH 243
                                         *************************************************************************** PP

                           TIGR00034 226 iilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesn 299
                                         ++lrGG+  pnyd+ +va ++++l ka+ k+++m+d+sh+nsnkd   q+ v+e+v++qi eG+++iiG+m+es+
  lcl|FitnessBrowser__Putida:PP_2324 244 VVLRGGNGkPNYDSVSVALCEQDLAKAKIKANIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVESH 318
                                         ******988****************************************************************** PP

                           TIGR00034 300 leeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339
                                         l+ G qs+    ++l+yG+s+tdaci+w  te+ lr +++++k
  lcl|FitnessBrowser__Putida:PP_2324 319 LNWGCQSIpknLDDLQYGVSITDACIDWSATEKTLRSMHAKLK 361
                                         ********63335789**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (370 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: 10.54
//
[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