Alignments for a candidate for aroG in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Klebsiella michiganensis M5al

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate BWI76_RS17075 BWI76_RS17075 3-deoxy-7-phosphoheptulonate synthase

Query= ecocyc::AROH-MONOMER
         (348 letters)



>FitnessBrowser__Koxy:BWI76_RS17075
          Length = 348

 Score =  607 bits (1566), Expect = e-178
 Identities = 300/347 (86%), Positives = 321/347 (92%)

Query: 1   MNRTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPC 60
           MN+TDELRTARIESLVTPAELA R+PV+  VA HV+ SRRRIE+ILNGED+RLLV+IGPC
Sbjct: 1   MNKTDELRTARIESLVTPAELAQRHPVSAEVAAHVSASRRRIERILNGEDRRLLVVIGPC 60

Query: 61  SIHDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNH 120
           SIHD+ AAMEYA RLQ +R +YQ +LEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNH
Sbjct: 61  SIHDIDAAMEYARRLQGMRERYQPQLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNH 120

Query: 121 GLELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSC 180
           GLELAR LLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSC
Sbjct: 121 GLELARSLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSC 180

Query: 181 PVGFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNY 240
           PVGFKNGTDGNTRIAVDAIRA+RASHMFLSPDK GQMTIYQTSGNPYGHIIMRGGKKPNY
Sbjct: 181 PVGFKNGTDGNTRIAVDAIRASRASHMFLSPDKQGQMTIYQTSGNPYGHIIMRGGKKPNY 240

Query: 241 HADDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMA 300
           HA DIAAA   L EFDLPE LVVDFSHGNCQKQHRRQLEVC DICQQIR GSTAIAGIMA
Sbjct: 241 HAADIAAAGQALAEFDLPEQLVVDFSHGNCQKQHRRQLEVCADICQQIRAGSTAIAGIMA 300

Query: 301 ESFLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASAVDTR 347
           ESFL+EGTQK+V  QPL +GQSITDPCL W+D+ERL+++LA+A  TR
Sbjct: 301 ESFLQEGTQKVVAGQPLAWGQSITDPCLSWDDSERLLDELAAATATR 347


Lambda     K      H
   0.320    0.135    0.399 

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: 473
Number of extensions: 5
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: 348
Length of database: 348
Length adjustment: 29
Effective length of query: 319
Effective length of database: 319
Effective search space:   101761
Effective search space used:   101761
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate BWI76_RS17075 BWI76_RS17075 (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.26334.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   9.5e-173  559.7   0.0   1.1e-172  559.5   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS17075  BWI76_RS17075 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS17075  BWI76_RS17075 3-deoxy-7-phosphoheptulonate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  559.5   0.0  1.1e-172  1.1e-172       1     341 [.       5     347 ..       5     348 .] 0.99

  Alignments for each domain:
  == domain 1  score: 559.5 bits;  conditional E-value: 1.1e-172
                               TIGR00034   1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrl 71 
                                             d+lr+++i++l+tP+el++++p+++++a++v  sr++i++il+G+d rllvviGPcsihd  aa+eya+rl
  lcl|FitnessBrowser__Koxy:BWI76_RS17075   5 DELRTARIESLVTPAELAQRHPVSAEVAAHVSASRRRIERILNGEDRRLLVVIGPCSIHDIDAAMEYARRL 75 
                                             799******************************************************************** PP

                               TIGR00034  72 kklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldt 142
                                             + ++e+++ +leivmr+yfekPrt+vGWkGli+dPdln+s++vn+Gl++ar lll+++elg+p+ate+ld+
  lcl|FitnessBrowser__Koxy:BWI76_RS17075  76 QGMRERYQPQLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNHGLELARSLLLQVNELGVPTATEFLDM 146
                                             *********************************************************************** PP

                               TIGR00034 143 ispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqv 213
                                             +++q++adl+swgaiGarttesq+hre+as+ls+pvgfkngtdG++++a+daira++a+h+fls++k+Gq+
  lcl|FitnessBrowser__Koxy:BWI76_RS17075 147 VTGQFIADLISWGAIGARTTESQIHREMASALSCPVGFKNGTDGNTRIAVDAIRASRASHMFLSPDKQGQM 217
                                             *********************************************************************** PP

                               TIGR00034 214 aivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqi 284
                                             +i++t+Gn++ghii+rGGkkpny+a+d+a++ + l +++l e+l++dfshgn++k+++rqlev++++++qi
  lcl|FitnessBrowser__Koxy:BWI76_RS17075 218 TIYQTSGNPYGHIIMRGGKKPNYHAADIAAAGQALAEFDLPEQLVVDFSHGNCQKQHRRQLEVCADICQQI 288
                                             *********************************************************************** PP

                               TIGR00034 285 aeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavker 341
                                             + G++ai+G+m es+l+eG+q++  +++l++G+s+td c++w+d+e+ll +la+a  +r
  lcl|FitnessBrowser__Koxy:BWI76_RS17075 289 RAGSTAIAGIMAESFLQEGTQKVvaGQPLAWGQSITDPCLSWDDSERLLDELAAATATR 347
                                             **********************98899**************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (348 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: 7.31
//
[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:

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