Alignments for a candidate for argB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for argB in Pedobacter sp. GW460-11-11-14-LB5

Align N-succinylglutamate kinase (EC 2.7.2.-) (characterized)
to candidate CA265_RS18510 CA265_RS18510 acetylglutamate kinase

Query= reanno::Btheta:352922
         (257 letters)



>FitnessBrowser__Pedo557:CA265_RS18510
          Length = 278

 Score =  278 bits (712), Expect = 7e-80
 Identities = 145/268 (54%), Positives = 190/268 (70%), Gaps = 17/268 (6%)

Query: 3   EKLTVIKVGGKIVEEEATLLQLLNDFAAISGHKVLVHGGGRSATKIAAQLGIESKMVNGR 62
           ++LT+IK+GG +++    L Q L DF A+ G K+LVHGGG+ AT++   LGIE+KM++GR
Sbjct: 4   KQLTIIKIGGNVIDNSENLHQFLLDFTALPGDKILVHGGGKIATELGESLGIEAKMIDGR 63

Query: 63  RITDAETLKVVTMVYGGLVNKNIVAGLQARGVNALGLTGADMNVIRSVKRPV-------- 114
           RITD ETL++VTMVY GL+NKN+VA LQA+G NA+GL+GAD NVIR+ KRPV        
Sbjct: 64  RITDIETLRIVTMVYAGLINKNMVAQLQAKGSNAIGLSGADGNVIRAKKRPVITKTYGAE 123

Query: 115 ------KEVDYGFVGDVEK--VDASLLADLIHKGVVPVMAPLTHDGQGNMLNTNADTIAG 166
                   +DYGFVGD+++  V ++ L  L+  G+VPV+  +THDG   +LNTNADTIA 
Sbjct: 124 SGPMAGAVIDYGFVGDLDENAVSSTTLESLLKAGLVPVLCAITHDGDTQLLNTNADTIAS 183

Query: 167 ETAKALSALFDVTLVYCFEKKGVLRDENDDDSVIPEITRAEFEQYVADGVIQGGMIPKLE 226
             A A+SAL++  LVYCFEKKGVL++ NDD SV+ EI   EFE   ADG +QGGMIPKL 
Sbjct: 184 SVAVAMSALYETRLVYCFEKKGVLKNVNDDGSVVREIKADEFEGLKADGTVQGGMIPKLH 243

Query: 227 NSFEAINAGVTEVVITLASAIKD-NEGT 253
           N+FEAI  GV+ V I  A  + +  EGT
Sbjct: 244 NAFEAIKKGVSAVYIGKADELAELAEGT 271


Lambda     K      H
   0.316    0.135    0.366 

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: 254
Number of extensions: 8
Number of successful extensions: 3
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: 257
Length of database: 278
Length adjustment: 25
Effective length of query: 232
Effective length of database: 253
Effective search space:    58696
Effective search space used:    58696
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate CA265_RS18510 CA265_RS18510 (acetylglutamate kinase)
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))

# 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/TIGR00761.hmm
# target sequence database:        /tmp/gapView.14861.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00761  [M=231]
Accession:   TIGR00761
Description: argB: acetylglutamate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.4e-60  189.9   3.7    2.7e-60  189.8   3.7    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS18510  CA265_RS18510 acetylglutamate ki


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS18510  CA265_RS18510 acetylglutamate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   3.7   2.7e-60   2.7e-60       2     231 .]       7     258 ..       6     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2.7e-60
                                  TIGR00761   2 iViKiGGaaiselleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlev 69 
                                                 +iKiGG++i++ +e+l + +  + +     ++vHGGg+  +el e lgie ++++g R+Td etl +
  lcl|FitnessBrowser__Pedo557:CA265_RS18510   7 TIIKIGGNVIDN-SENLHQFLLDFTALPGDKILVHGGGKIATELGESLGIEAKMIDGRRITDIETLRI 73 
                                                69*********6.999999999999998888************************************* PP

                                  TIGR00761  70 vemvligkvnkelvallekhgikavGltgkDgqlltae...kldke.............dlgyvGeik 121
                                                v+mv++g +nk++va+l+ +g +a+Gl+g+Dg+++ a+    ++k              d+g+vG+++
  lcl|FitnessBrowser__Pedo557:CA265_RS18510  74 VTMVYAGLINKNMVAQLQAKGSNAIGLSGADGNVIRAKkrpVITKTygaesgpmagaviDYGFVGDLD 141
                                                **************************************887666668899***************996 PP

                                  TIGR00761 122 ..kvnkelleallkagiipviaslaldeegqllNvnaDtaAaelAaaleA...ekLvlLtdvaGileg 184
                                                  +v+   le+llkag +pv+ ++  d + qllN+naDt+A+ +A a+ A    +Lv+  +++G+l++
  lcl|FitnessBrowser__Pedo557:CA265_RS18510 142 enAVSSTTLESLLKAGLVPVLCAITHDGDTQLLNTNADTIASSVAVAMSAlyeTRLVYCFEKKGVLKN 209
                                                2369*****************************************9999955458************* PP

                                  TIGR00761 185 ..dkksliseleleeieqlikqavikgGmipKveaalealesgvkkvvi 231
                                                  d  s+++e++++e e l   + ++gGmipK+++a ea+++gv++v i
  lcl|FitnessBrowser__Pedo557:CA265_RS18510 210 vnDDGSVVREIKADEFEGLKADGTVQGGMIPKLHNAFEAIKKGVSAVYI 258
                                                998889***************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (278 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: 00:00:00.00
# 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