Alignments for a candidate for proB in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Dyella japonica UNC79MFTsu3.2

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate N515DRAFT_3772 N515DRAFT_3772 glutamate 5-kinase

Query= BRENDA::P0A7B5
         (367 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3772
          Length = 380

 Score =  274 bits (701), Expect = 3e-78
 Identities = 157/360 (43%), Positives = 220/360 (61%), Gaps = 5/360 (1%)

Query: 8   VVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPA 67
           V+K+G+++L      L   H   L       HA G ++V+V+SGA+AAGR  L    LP 
Sbjct: 17  VLKVGSNLLAADGGGLTPRHARALAAFIGDSHAQGRQVVLVSSGAVAAGRALLRERALPG 76

Query: 68  T-IASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLD 126
             +A++Q LAA+GQ+ +I LW+   S+    V Q+LLT  D+  R R+LNAR TLR LL 
Sbjct: 77  DDLAARQALAALGQAPMIALWQ---SLSPRPVAQVLLTHDDLRHRRRYLNARATLRELLL 133

Query: 127 NNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAE 186
            +++PV+NEND VA  E+K+GDNDNL+A+ A L  AD LL+ +D   LY ADPR  P A 
Sbjct: 134 LDVLPVVNENDTVAVDELKLGDNDNLAAIVAALVDADLLLIASDIDALYDADPRRVPSAV 193

Query: 187 LIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVM 246
            +  V  +   + A+AG S S +GTGGM TKL+AA  A  AG+ T++  G     +  + 
Sbjct: 194 PVPHVSTLTAEVMAMAGGSGSAVGTGGMHTKLEAAVKAGAAGVPTVLFDGRNTETVAALA 253

Query: 247 EGISVGTLFHAQATPLENRKRWIFGAPPA-GEITVDEGATAAILERGSSLLPKGIKSVTG 305
            G   GTLF A  + ++ RK W+  AP A G I VD+GA  A+    +SLLP GI    G
Sbjct: 254 AGQLHGTLFDAPRSRMQARKYWLRHAPAAPGSILVDDGAARALAGGRASLLPGGIVGADG 313

Query: 306 NFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMI 365
            F RG+++ I ++  R +A G+S+Y +  +RR+AG HS  IDA+LGY YG   VHRDD++
Sbjct: 314 EFHRGDMVEIVDVTRRPVARGLSQYGAAEVRRLAGRHSSAIDAVLGYSYGAEIVHRDDLV 373


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: 407
Number of extensions: 20
Number of successful extensions: 4
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: 380
Length adjustment: 30
Effective length of query: 337
Effective length of database: 350
Effective search space:   117950
Effective search space used:   117950
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: 50 (23.9 bits)

Align candidate N515DRAFT_3772 N515DRAFT_3772 (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.6235.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   7.7e-122  392.9   0.0   8.8e-122  392.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772  N515DRAFT_3772 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3772  N515DRAFT_3772 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.7   0.0  8.8e-122  8.8e-122       2     362 ..      15     373 ..      14     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 392.7 bits;  conditional E-value: 8.8e-122
                                    TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperp.kkla 66 
                                                  r V+K+Gs++L+++ g l+  + ++l++ +   +++G++vv+vsSGavaaG + L     p  +la
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772  15 RAVLKVGSNLLAADGGGLTPRHARALAAFIGDSHAQGRQVVLVSSGAVAAGRALLRERALPgDDLA 80 
                                                  78*******************************************************9999458** PP

                                    TIGR01027  67 ekQalaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNEN 132
                                                   +Qalaa GQ+ +++l+++l     + vaQ+LLt++dl++r+rylNar+tl+ell l+v+p+vNEN
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772  81 ARQALAALGQAPMIALWQSL---SPRPVAQVLLTHDDLRHRRRYLNARATLRELLLLDVLPVVNEN 143
                                                  *****************976...5689*************************************** PP

                                    TIGR01027 133 DtvaveeikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkava 198
                                                  Dtvav+e+k+GDND+L+a+vaalv+AdlL++ +d+d+Lydadpr+ p A ++++v+ +++e+ a+a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772 144 DTVAVDELKLGDNDNLAAIVAALVDADLLLIASDIDALYDADPRRVPSAVPVPHVSTLTAEVMAMA 209
                                                  ****************************************************************** PP

                                    TIGR01027 199 gssgssvGTGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqw 264
                                                  g+sgs+vGTGGm+tKleaa  A +agv++++  g++ e++a+l++++  gtlf a ++++++rk w
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772 210 GGSGSAVGTGGMHTKLEAAVKAGAAGVPTVLFDGRNTETVAALAAGQLHGTLFDAPRSRMQARKYW 275
                                                  ****************************************************************** PP

                                    TIGR01027 265 ilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysse 330
                                                  + +a++a G+i+vd+ga++al   ++sLlp g+v+  g+F+rg++vei++   + +++gl++y ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772 276 LRHAPAAPGSILVDDGAARALAGGRASLLPGGIVGADGEFHRGDMVEIVDVTRRPVARGLSQYGAA 341
                                                  ****************************************************************** PP

                                    TIGR01027 331 elekikglkseeiedvLgyekkeevvhrdnlv 362
                                                  e+++++g++s+ i++vLgy++ +e+vhrd+lv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3772 342 EVRRLAGRHSSAIDAVLGYSYGAEIVHRDDLV 373
                                                  ******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (380 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.13
//
[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