Aligments for a candidate for aroG in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments 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::P0AB91
         (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.5930.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.81
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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