Aligments for a candidate for proB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Aligments for a candidate for proB in Klebsiella michiganensis M5al

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate BWI76_RS05840 BWI76_RS05840 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05840 BWI76_RS05840 glutamate
           5-kinase
          Length = 367

 Score =  680 bits (1754), Expect = 0.0
 Identities = 348/367 (94%), Positives = 358/367 (97%)

Query: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHL 60
           MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHA GHRIVIVTSGAIAAGREHL
Sbjct: 1   MSDSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAMGHRIVIVTSGAIAAGREHL 60

Query: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120
           GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT
Sbjct: 61  GYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDT 120

Query: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPR 180
           LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQ+GL+TADPR
Sbjct: 121 LRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQQGLFTADPR 180

Query: 181 SNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPG 240
           +NPQAELIKDVYGIDDALRAIAGDSVSGLGTGGM TKLQAADVACRAGIDTIIAAGS+PG
Sbjct: 181 NNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMGTKLQAADVACRAGIDTIIAAGSRPG 240

Query: 241 VIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPAGEITVDEGATAAILERGSSLLPKGI 300
           VIGDVMEG+SVGT FHAQ +PLENRKRWIFGAPPAGEITVD GAT AILERGSSLLPKGI
Sbjct: 241 VIGDVMEGVSVGTRFHAQESPLENRKRWIFGAPPAGEITVDAGATQAILERGSSLLPKGI 300

Query: 301 KSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVH 360
           K++TGNFSRGEVIRI +LEGRDIAHGVSRYNSDALRRIAG HSQ+IDAILGYEYGPVAVH
Sbjct: 301 KTITGNFSRGEVIRIRSLEGRDIAHGVSRYNSDALRRIAGQHSQQIDAILGYEYGPVAVH 360

Query: 361 RDDMITR 367
           RDDMI R
Sbjct: 361 RDDMIIR 367


Lambda     K      H
   0.318    0.135    0.384 

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: 587
Number of extensions: 13
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: 367
Length of database: 367
Length adjustment: 30
Effective length of query: 337
Effective length of database: 337
Effective search space:   113569
Effective search space used:   113569
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 BWI76_RS05840 BWI76_RS05840 (glutamate 5-kinase)
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# 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/TIGR01027.hmm
# target sequence database:        /tmp/gapView.23811.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.9e-159  515.0   0.3   6.7e-159  514.8   0.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS05840  BWI76_RS05840 glutamate 5-kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS05840  BWI76_RS05840 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  514.8   0.3  6.7e-159  6.7e-159       1     363 []       5     366 ..       5     366 .. 0.99

  Alignments for each domain:
  == domain 1  score: 514.8 bits;  conditional E-value: 6.7e-159
                               TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQal 71 
                                             +++VvKlG+s+Lt +s++l+r++++elv+q+a+l+++Gh++viv+SGa+aaG e+Lg+pe p+++a+kQ+l
  lcl|FitnessBrowser__Koxy:BWI76_RS05840   5 QTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAMGHRIVIVTSGAIAAGREHLGYPELPATIASKQLL 75 
                                             689******************************************************************** PP

                               TIGR01027  72 aaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikf 142
                                             aaVGQ+rL++l+e+lfs+yg++v+Q+LLtrad+++rer+lNar+tl++ll++++vp++NEND+va++eik+
  lcl|FitnessBrowser__Koxy:BWI76_RS05840  76 AAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNIVPVINENDAVATAEIKV 146
                                             *********************************************************************** PP

                               TIGR01027 143 GDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtK 213
                                             GDND+Lsal a+l +Ad L+lltd++gL++adpr+np+A+li+ v  i+++l+a+ag+s s +GTGGm tK
  lcl|FitnessBrowser__Koxy:BWI76_RS05840 147 GDNDNLSALAAILAGADKLLLLTDQQGLFTADPRNNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMGTK 217
                                             *********************************************************************** PP

                               TIGR01027 214 leaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeea 284
                                             l+aa++A+rag+++iia+g++p  i d++e+++vgt f+a+++ l+nrk+wi+ a+ a G+i+vd+ga++a
  lcl|FitnessBrowser__Koxy:BWI76_RS05840 218 LQAADVACRAGIDTIIAAGSRPGVIGDVMEGVSVGTRFHAQESPLENRKRWIFGAPPA-GEITVDAGATQA 287
                                             ****************************************************988877.************ PP

                               TIGR01027 285 llekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeev 355
                                             +le+g+sLlp+g+  ++gnFsrgev++i++ eg++i++g+++y+s++l++i+g++s++i+++Lgye+  ++
  lcl|FitnessBrowser__Koxy:BWI76_RS05840 288 ILERGSSLLPKGIKTITGNFSRGEVIRIRSLEGRDIAHGVSRYNSDALRRIAGQHSQQIDAILGYEYGPVA 358
                                             *********************************************************************** PP

                               TIGR01027 356 vhrdnlvl 363
                                             vhrd++++
  lcl|FitnessBrowser__Koxy:BWI76_RS05840 359 VHRDDMII 366
                                             *****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (367 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: 10.19
//
[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