GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Caulobacter crescentus NA1000

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate CCNA_01463 CCNA_01463 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>FitnessBrowser__Caulo:CCNA_01463
          Length = 369

 Score =  446 bits (1148), Expect = e-130
 Identities = 215/344 (62%), Positives = 268/344 (77%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DDLRI++++ L PP  ++ + PAT + A  V  AR+A+H+IL G DDRL+VVIGPCSIHD
Sbjct: 17  DDLRIEKLQTLSPPAQVIGEAPATSSVAEIVGGARQAVHQILHGQDDRLVVVIGPCSIHD 76

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
           P AA +YA RL A RE    ELE++MRVYFEKPRTTVGWKGLINDP +D  F+INDGLR+
Sbjct: 77  PKAAIDYARRLAAERERHAGELEVIMRVYFEKPRTTVGWKGLINDPGLDGGFRINDGLRL 136

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR++LLD++  GLPAA EFLD+ TPQY+ADL+SWGAIGARTTESQ+HRELASGLSCPVGF
Sbjct: 137 ARRVLLDVSAQGLPAACEFLDVTTPQYIADLVSWGAIGARTTESQIHRELASGLSCPVGF 196

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245
           KNGT+G +K+A+DA+ AA  PH FL+VTK G +AI  T+GNGDCH++LRGGK PNY A  
Sbjct: 197 KNGTNGDVKIAVDAVMAASQPHHFLAVTKEGRAAIATTTGNGDCHLVLRGGKTPNYDAAS 256

Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305
           VA   E L+KAGLP ++M+D SHANS K  + Q  V ADVC Q+A G   ++GVM+ES+L
Sbjct: 257 VAAAAEVLSKAGLPQRLMVDVSHANSGKNHENQPAVIADVCAQVATGASPVMGVMIESNL 316

Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           V G Q +  G+ L YG+S+TDAC+ WE +  LL  LA AV+A R
Sbjct: 317 VAGRQDIVQGQGLTYGQSVTDACVDWETSVRLLDDLAGAVRAGR 360


Lambda     K      H
   0.317    0.134    0.397 

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: 427
Number of extensions: 12
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: 350
Length of database: 369
Length adjustment: 29
Effective length of query: 321
Effective length of database: 340
Effective search space:   109140
Effective search space used:   109140
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CCNA_01463 CCNA_01463 (3-deoxy-7-phosphoheptulonate synthase)
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.3259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.5e-162  524.0   0.0   7.6e-162  523.8   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01463  CCNA_01463 3-deoxy-7-phosphohept


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01463  CCNA_01463 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  523.8   0.0  7.6e-162  7.6e-162       1     340 [.      17     358 ..      17     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 523.8 bits;  conditional E-value: 7.6e-162
                             TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 
                                           ddlri+k++ l +P++++ + p+t+++ae v  +r+++++il+G+ddrl+vviGPcsihdp+aa++ya+rl++
  lcl|FitnessBrowser__Caulo:CCNA_01463  17 DDLRIEKLQTLSPPAQVIGEAPATSSVAEIVGGARQAVHQILHGQDDRLVVVIGPCSIHDPKAAIDYARRLAA 89 
                                           799********************************************************************** PP

                             TIGR00034  74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispq 146
                                            +e+   +le++mrvyfekPrttvGWkGlindP l++ f++n+Glr+ar++lld+   glp+a+e+ld+ +pq
  lcl|FitnessBrowser__Caulo:CCNA_01463  90 ERERHAGELEVIMRVYFEKPRTTVGWKGLINDPGLDGGFRINDGLRLARRVLLDVSAQGLPAACEFLDVTTPQ 162
                                           ************************************************************************* PP

                             TIGR00034 147 yladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetk 219
                                           y+adl+swgaiGarttesq+hrelasgls+pvgfkngt+G++k+a+da+ aa+++h+fl+vtk+G++ai +t+
  lcl|FitnessBrowser__Caulo:CCNA_01463 163 YIADLVSWGAIGARTTESQIHRELASGLSCPVGFKNGTNGDVKIAVDAVMAASQPHHFLAVTKEGRAAIATTT 235
                                           ************************************************************************* PP

                             TIGR00034 220 GnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaii 292
                                           Gn d+h++lrGGk+pnyda++va++ e l+kagl ++lm+d+sh+ns k++++q++v ++v++q+a+G   ++
  lcl|FitnessBrowser__Caulo:CCNA_01463 236 GNGDCHLVLRGGKTPNYDAASVAAAAEVLSKAGLPQRLMVDVSHANSGKNHENQPAVIADVCAQVATGASPVM 308
                                           ************************************************************************* PP

                             TIGR00034 293 GvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavke 340
                                           Gvmiesnl+ G+q++  +++l+yG+svtdac++we++ +ll +la av++
  lcl|FitnessBrowser__Caulo:CCNA_01463 309 GVMIESNLVAGRQDIvqGQGLTYGQSVTDACVDWETSVRLLDDLAGAVRA 358
                                           **************988899***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (369 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.53
//
[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:

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