Alignments for a candidate for proB in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Sinorhizobium meliloti 1021

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate SMc03776 SMc03776 gamma-glutamyl kinase

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



>FitnessBrowser__Smeli:SMc03776
          Length = 393

 Score =  322 bits (824), Expect = 1e-92
 Identities = 184/362 (50%), Positives = 242/362 (66%), Gaps = 8/362 (2%)

Query: 11  RLVVKIGSALLVDPEGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKLAKG 70
           R+V+KIGSALLVD    +++ WL+ + ADIAA    G ++ VVSSGAIALG   L L  G
Sbjct: 13  RVVIKIGSALLVDRRTGLKKSWLDALCADIAALRAKGVEVLVVSSGAIALGRTVLDLPAG 72

Query: 71  GRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATLGRL 130
               LE++QAAAA GQI L++ W+E L+ + + A Q+L+TL D E+RRRYLNA AT+G+L
Sbjct: 73  A-LKLEESQAAAAVGQIVLARAWSESLSTHAIVAGQILLTLGDTEERRRYLNARATIGQL 131

Query: 131 LSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNPAL-PG 189
           L LG VP+INEND+VAT EIR+GDNDRLAARVA    A  +VLLSDIDGLY   P L P 
Sbjct: 132 LKLGSVPIINENDTVATTEIRYGDNDRLAARVATMVGADLLVLLSDIDGLYTAPPHLDPN 191

Query: 190 AVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANGRVDRPLS 249
           A  +  V  I   +E MA  G+AS +  GGM +KI+A +IA +AG ++ IA+G+ D PL+
Sbjct: 192 ARFLETVAEITPEIEAMAG-GAASELSRGGMRTKIDAGKIATTAGCAMIIASGKPDHPLA 250

Query: 250 ---ADARHTVFLPE-KRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIGATAIR 305
              A AR + F P      ARK W+AG+L   GS+ +DAGA  AL  G+SLL  G   + 
Sbjct: 251 AIEAGARSSWFAPSGSPVTARKTWIAGQLLPAGSLSIDAGAETALRSGKSLLPAGVRQVT 310

Query: 306 GMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVHRNHM 364
           G F RGD + I G +G  IARGL+ YDA +A+ I G +S +   ILGYA R+ +VHR+ +
Sbjct: 311 GSFSRGDTIAIIGASGREIARGLAGYDADEARQIAGKKSAEIAAILGYAGRTAMVHRDDL 370

Query: 365 AL 366
            +
Sbjct: 371 VM 372


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: 409
Number of extensions: 21
Number of successful extensions: 5
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: 393
Length adjustment: 30
Effective length of query: 337
Effective length of database: 363
Effective search space:   122331
Effective search space used:   122331
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: 50 (23.9 bits)

Align candidate SMc03776 SMc03776 (gamma-glutamyl 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.10495.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.5e-122  394.4   0.3   2.9e-122  394.2   0.3    1.0  1  lcl|FitnessBrowser__Smeli:SMc03776  SMc03776 gamma-glutamyl kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03776  SMc03776 gamma-glutamyl kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.2   0.3  2.9e-122  2.9e-122       1     362 [.      12     371 ..      12     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 394.2 bits;  conditional E-value: 2.9e-122
                           TIGR01027   1 kriVvKlGsssLteesgklkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVG 75 
                                         +r+V+K+Gs++L++  + lk+s l +l++++a+l+++G ev++vsSGa+a G + L+lp    kl+e Qa+aaVG
  lcl|FitnessBrowser__Smeli:SMc03776  12 RRVVIKIGSALLVDRRTGLKKSWLDALCADIAALRAKGVEVLVVSSGAIALGRTVLDLPAGALKLEESQAAAAVG 86 
                                         59************************************************************************* PP

                           TIGR01027  76 QgrLmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsa 150
                                         Q  L +++++++s++ +  +QiLLt  d ++r+rylNar+t+ +ll+lg vpi+NENDtva++ei+ GDND+L+a
  lcl|FitnessBrowser__Smeli:SMc03776  87 QIVLARAWSESLSTHAIVAGQILLTLGDTEERRRYLNARATIGQLLKLGSVPIINENDTVATTEIRYGDNDRLAA 161
                                         *************************************************************************** PP

                           TIGR01027 151 lvaalveAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragv 225
                                          va++v+AdlLvll+d+dgLy+a p+ +p+A+++e+v ei+ e++a+ag+++s++  GGmrtK+ a ++A++ag 
  lcl|FitnessBrowser__Smeli:SMc03776 162 RVATMVGADLLVLLSDIDGLYTAPPHLDPNARFLETVAEITPEIEAMAGGAASELSRGGMRTKIDAGKIATTAGC 236
                                         *************************************************************************** PP

                           TIGR01027 226 eviiasgekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvev 300
                                          +iiasg+ p++ ++++e  a  + f+++ + + +rk+wi+ ++ ++G++ +d+gae+al++ gksLlpagv +v
  lcl|FitnessBrowser__Smeli:SMc03776 237 AMIIASGK-PDHPLAAIEAGARSSWFAPSGSPVTARKTWIAGQLLPAGSLSIDAGAETALRS-GKSLLPAGVRQV 309
                                         *****998.67777788888999**************************************9.************ PP

                           TIGR01027 301 egnFsrgevveilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlv 362
                                         +g+Fsrg+++ i   +g+ei++gl+ y+++e ++i+g+ks+ei+++Lgy  ++  vhrd+lv
  lcl|FitnessBrowser__Smeli:SMc03776 310 TGSFSRGDTIAIIGASGREIARGLAGYDADEARQIAGKKSAEIAAILGYAGRTAMVHRDDLV 371
                                         ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (393 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.84
//
[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