Alignments for a candidate for proB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Sphingomonas koreensis DSMZ 15582

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate Ga0059261_3512 Ga0059261_3512 glutamate 5-kinase

Query= reanno::Korea:Ga0059261_3512
         (367 letters)



>FitnessBrowser__Korea:Ga0059261_3512
          Length = 367

 Score =  700 bits (1806), Expect = 0.0
 Identities = 367/367 (100%), Positives = 367/367 (100%)

Query: 1   MHLFPPASCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIAL 60
           MHLFPPASCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIAL
Sbjct: 1   MHLFPPASCPRLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIAL 60

Query: 61  GARRLKLAKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRY 120
           GARRLKLAKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRY
Sbjct: 61  GARRLKLAKGGRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRY 120

Query: 121 LNAAATLGRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGL 180
           LNAAATLGRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGL
Sbjct: 121 LNAAATLGRLLSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGL 180

Query: 181 YDRNPALPGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIA 240
           YDRNPALPGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIA
Sbjct: 181 YDRNPALPGAVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIA 240

Query: 241 NGRVDRPLSADARHTVFLPEKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIG 300
           NGRVDRPLSADARHTVFLPEKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIG
Sbjct: 241 NGRVDRPLSADARHTVFLPEKRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIG 300

Query: 301 ATAIRGMFFRGDLVTIEGPNGPIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVH 360
           ATAIRGMFFRGDLVTIEGPNGPIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVH
Sbjct: 301 ATAIRGMFFRGDLVTIEGPNGPIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVH 360

Query: 361 RNHMALL 367
           RNHMALL
Sbjct: 361 RNHMALL 367


Lambda     K      H
   0.319    0.134    0.377 

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: 588
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: 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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate Ga0059261_3512 Ga0059261_3512 (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.10490.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-107  344.5   0.4   4.3e-107  344.3   0.4    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3512  Ga0059261_3512 glutamate 5-kinas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3512  Ga0059261_3512 glutamate 5-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.3   0.4  4.3e-107  4.3e-107       2     362 ..      11     365 ..      10     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 344.3 bits;  conditional E-value: 4.3e-107
                                 TIGR01027   2 riVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglper.pkklaekQ 69 
                                               r+VvK+Gs++L++++g ++r  l+ +++++a++ +aG+++ +vsSGa+a G+++L l +   ++l++ Q
  lcl|FitnessBrowser__Korea:Ga0059261_3512  11 RLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKLAKGgRASLEDAQ 79 
                                               79******************************************************98862579***** PP

                                 TIGR01027  70 alaaVGQgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvave 138
                                               a+aa GQ +L + + ++++  gl+ aQ+L t +dl++r+rylNa +tl +ll+lgvvp++NEND+va++
  lcl|FitnessBrowser__Korea:Ga0059261_3512  80 AAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATLGRLLSLGVVPVINENDSVATA 148
                                               ********************************************************************* PP

                                 TIGR01027 139 eikfGDNDtLsalvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagss.gssvG 206
                                               ei+fGDND+L+a va+  +A   vll+d+dgLyd++p   p A  i++ve+i+  ++++a ++ +s +G
  lcl|FitnessBrowser__Korea:Ga0059261_3512 149 EIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNP-ALPGAVHIPVVERIDGRVEGMADRGsASGMG 216
                                               *************************************.99******************998763566** PP

                                 TIGR01027 207 TGGmrtKleaaelAsragveviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGki 275
                                                GGm +K+eaa++A++agv   ia+g+    + + l+  a +t+f ++k+  ++rk+w++  ++akG+i
  lcl|FitnessBrowser__Korea:Ga0059261_3512 217 SGGMVSKIEAARIAASAGVSLAIANGR----VDRPLSADARHTVFLPEKR-TRARKAWLAGRLTAKGSI 280
                                               *************************99....688899999*******977.89**************** PP

                                 TIGR01027 276 ivdegaeeallekgksLlpagvvevegnFsrgevveilaeegqeigkglvnysseelekikglkseeie 344
                                               ivd+ga++al+e g+sLl+ g ++++g F rg+ v+i  ++g  i++gl++y++ + + i g++s++  
  lcl|FitnessBrowser__Korea:Ga0059261_3512 281 IVDAGAAQALTE-GRSLLAIGATAIRGMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQG 347
                                               ***********9.***************************98.79************************ PP

                                 TIGR01027 345 dvLgyekkeevvhrdnlv 362
                                               ++Lgy  +++ vhr++++
  lcl|FitnessBrowser__Korea:Ga0059261_3512 348 EILGYAPRSTLVHRNHMA 365
                                               ***************997 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.55
//
[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