Alignments for a candidate for aroG in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Paraburkholderia phymatum STM815

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012403405.1 BPHY_RS20705 3-deoxy-7-phosphoheptulonate synthase

Query= BRENDA::C3TIE2
         (350 letters)



>NCBI__GCF_000020045.1:WP_012403405.1
          Length = 374

 Score =  405 bits (1041), Expect = e-118
 Identities = 201/345 (58%), Positives = 252/345 (73%), Gaps = 1/345 (0%)

Query: 6   DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65
           DD RI  ++ L+ P  LL++ P   +    V  +R  I  IL   DDRL+VV+GPCSIHD
Sbjct: 26  DDTRIGAVRPLISPALLLDELPCPPDVQTLVEKSRVEIADILHDRDDRLVVVVGPCSIHD 85

Query: 66  PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125
              A EYA +L    E L+D+L IVMRVYFEKPRTTVGWKG INDP +D SF+IN+GLR 
Sbjct: 86  HDQAMEYAHKLRTAAEALRDDLMIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRR 145

Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185
           AR+LLL+I+  GLP   EFLD+++PQY+ADL++WGAIGARTTESQ HR+LASGLSCP+GF
Sbjct: 146 ARELLLEISGLGLPTGTEFLDLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGF 205

Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-PNYSAK 244
           KNGTDG +++A DAI AA A H F+ +TK G +AI  T GN D H+ILRGGK+ PNY A 
Sbjct: 206 KNGTDGGVQIAADAIVAAAASHAFMGMTKMGMAAIFETRGNDDAHVILRGGKKGPNYDAA 265

Query: 245 HVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESH 304
            V E    L K GL  QVM+D SHANS+K  ++Q++V  D+  Q++GG+K I+GVM+ESH
Sbjct: 266 GVEEACTALRKVGLREQVMVDCSHANSNKSHERQIEVAQDLANQLSGGDKRIVGVMIESH 325

Query: 305 LVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349
           L  G Q L+ G PLA+G SITDACIGW  T+ +L  LA AV+ARR
Sbjct: 326 LEAGRQDLKPGVPLAHGVSITDACIGWAQTEPVLETLAQAVRARR 370


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: 410
Number of extensions: 12
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: 350
Length of database: 374
Length adjustment: 29
Effective length of query: 321
Effective length of database: 345
Effective search space:   110745
Effective search space used:   110745
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 WP_012403405.1 BPHY_RS20705 (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.8952.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-157  509.8   0.0   1.6e-157  509.6   0.0    1.0  1  lcl|NCBI__GCF_000020045.1:WP_012403405.1  BPHY_RS20705 3-deoxy-7-phosphohe


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012403405.1  BPHY_RS20705 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.6   0.0  1.6e-157  1.6e-157       1     342 []      26     370 ..      26     370 .. 0.99

  Alignments for each domain:
  == domain 1  score: 509.6 bits;  conditional E-value: 1.6e-157
                                 TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 
                                               dd+ri ++ +l++P+ l  + p  +++++ v+ksr eiadil+ +ddrl+vv+GPcsihd   a+eya+
  lcl|NCBI__GCF_000020045.1:WP_012403405.1  26 DDTRIGAVRPLISPALLLDELPCPPDVQTLVEKSRVEIADILHDRDDRLVVVVGPCSIHDHDQAMEYAH 94 
                                               7999***************************************************************** PP

                                 TIGR00034  70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138
                                               +l++ ae l+ddl ivmrvyfekPrttvGWkG indP l++sf++n+Glr ar+lll++  lglp++te
  lcl|NCBI__GCF_000020045.1:WP_012403405.1  95 KLRTAAEALRDDLMIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRRARELLLEISGLGLPTGTE 163
                                               ********************************************************************* PP

                                 TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207
                                               +ld  spqy+adl++wgaiGarttesq hr+lasgls+p+gfkngtdG++++a dai aaaa+h f+++
  lcl|NCBI__GCF_000020045.1:WP_012403405.1 164 FLDLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGFKNGTDGGVQIAADAIVAAAASHAFMGM 232
                                               ********************************************************************* PP

                                 TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275
                                               tk G +ai et+Gn+d+h+ilrGGkk pnyda+ v+e++  l+k+gl+e++m+d+sh+nsnk ++rq+e
  lcl|NCBI__GCF_000020045.1:WP_012403405.1 233 TKMGMAAIFETRGNDDAHVILRGGKKgPNYDAAGVEEACTALRKVGLREQVMVDCSHANSNKSHERQIE 301
                                               ********************************************************************* PP

                                 TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342
                                               va+++++q++ G+k i+Gvmies+le G+q+l  + +l++G+s+tdacigw +te +l+ la+av++rr
  lcl|NCBI__GCF_000020045.1:WP_012403405.1 302 VAQDLANQLSGGDKRIVGVMIESHLEAGRQDLkpGVPLAHGVSITDACIGWAQTEPVLETLAQAVRARR 370
                                               ********************************656789****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (374 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: 8.47
//
[ok]

This GapMind analysis is from Apr 10 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