GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisG in Chlorobium limicola DSM 245

Align ATP phosphoribosyltransferase (EC 2.4.2.17) (characterized)
to candidate WP_012467061.1 CLIM_RS10900 ATP phosphoribosyltransferase

Query= reanno::DvH:209044
         (293 letters)



>NCBI__GCF_000020465.1:WP_012467061.1
          Length = 292

 Score =  314 bits (804), Expect = 2e-90
 Identities = 156/287 (54%), Positives = 208/287 (72%), Gaps = 1/287 (0%)

Query: 7   MKLGIPKGSLEEATINLLARSGWKIRKHHRNYFPEINDPELTARLCRVQEIPRYIEDGIL 66
           +KLG+PKGSL+++T++L A +G+      R+YFP I+D EL A L R QE+  Y+E G  
Sbjct: 6   LKLGLPKGSLQDSTLDLFAHAGFHFSVQSRSYFPSIDDDELEAILIRAQEMAHYVELGAF 65

Query: 67  DVGLTGKDWLLETGSDVVVVSDLVYSKVSNRPARWVLAVAGDSPYTRPEDLAGKRIATEL 126
           DVGLTGKDW++ET ++VV V+DLVYSK S RP RWVLAV   S     +DL GK IATE+
Sbjct: 66  DVGLTGKDWIIETDAEVVEVADLVYSKASMRPVRWVLAVPESSSINSVKDLEGKHIATEV 125

Query: 127 LGVTKRYFADAGIEVNVQYSWGATEAKVVEGLADAIVEVTETGTTIKAHGLRIISEVLLT 186
           + +TK+Y A  G+  +V++SWGATE K  + LADAIVEVTETG++++A+ LRI+  +L +
Sbjct: 126 VNITKKYLAKHGVNASVEFSWGATEVKPPD-LADAIVEVTETGSSLRANKLRIVDTILES 184

Query: 187 NTVLIANRAAWEDPCRRRKIEQIDLLLQGALRADSLVGLKMNVPTRCLDAVLDQLPSLNS 246
           NT LIAN+A+W DP +R KIE + +LLQGA+ A   VGLKMN P   LDAVL  +P+L  
Sbjct: 185 NTKLIANKASWNDPWKREKIESMAMLLQGAINAQGKVGLKMNTPKASLDAVLSIIPALRQ 244

Query: 247 PTVAGLRDNTWFAVEIVVDNGVVRDLIPRLREAGAEGIIEYALNKVI 293
           PTV+ L D  W A+E++V   +VR LIP L+ AGAEGI EY +NK+I
Sbjct: 245 PTVSHLADEGWVALEVIVTEKIVRKLIPELKRAGAEGIFEYDINKLI 291


Lambda     K      H
   0.319    0.137    0.402 

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: 272
Number of extensions: 8
Number of successful extensions: 2
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: 293
Length of database: 292
Length adjustment: 26
Effective length of query: 267
Effective length of database: 266
Effective search space:    71022
Effective search space used:    71022
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_012467061.1 CLIM_RS10900 (ATP phosphoribosyltransferase)
to HMM TIGR00070 (hisG: ATP phosphoribosyltransferase (EC 2.4.2.17))

# 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/TIGR00070.hmm
# target sequence database:        /tmp/gapView.14037.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00070  [M=183]
Accession:   TIGR00070
Description: hisG: ATP phosphoribosyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.2e-58  184.1   0.0    1.6e-58  183.6   0.0    1.2  1  lcl|NCBI__GCF_000020465.1:WP_012467061.1  CLIM_RS10900 ATP phosphoribosylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012467061.1  CLIM_RS10900 ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6   0.0   1.6e-58   1.6e-58       1     183 []       6     190 ..       6     190 .. 0.98

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.6e-58
                                 TIGR00070   1 lriAlpKGrleeetlkllekaglklskkeerkliasaedeevevlllrakdiptyvekgaadlGitGkD 69 
                                               l+++lpKG+l+++tl+l+++ag+++s ++ r+++ s++d+e+e++l+ra++++ yve ga+d+G+tGkD
  lcl|NCBI__GCF_000020465.1:WP_012467061.1   6 LKLGLPKGSLQDSTLDLFAHAGFHFSVQS-RSYFPSIDDDELEAILIRAQEMAHYVELGAFDVGLTGKD 73 
                                               79**************************9.*************************************** PP

                                 TIGR00070  70 lleEseadvvelldlgfgkc.....klvlAvpeesdvesledlkegkriATkypnltreylekkgvkve 133
                                               ++ E +a+vve++dl ++k+     ++vlAvpe+s+++s++dl+ gk iAT+ +n+t++yl+k+gv+++
  lcl|NCBI__GCF_000020465.1:WP_012467061.1  74 WIIETDAEVVEVADLVYSKAsmrpvRWVLAVPESSSINSVKDLE-GKHIATEVVNITKKYLAKHGVNAS 141
                                               ***************99999888889******************.9*********************** PP

                                 TIGR00070 134 ivkleGavElapllgladaIvDivetGttLrengLkiieeilessarlia 183
                                               +  ++Ga+E++p  +ladaIv ++etG++Lr+n+L+i+++iles+++lia
  lcl|NCBI__GCF_000020465.1:WP_012467061.1 142 VEFSWGATEVKP-PDLADAIVEVTETGSSLRANKLRIVDTILESNTKLIA 190
                                               ************.9**********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (183 nodes)
Target sequences:                          1  (292 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.65
//
[ok]

This GapMind analysis is from Apr 10 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:

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:

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:

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:

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