GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Sinorhizobium meliloti 1021

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate SMc02570 SMc02570 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= curated2:A7HSH1
         (243 letters)



>lcl|FitnessBrowser__Smeli:SMc02570 SMc02570
           1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase
          Length = 247

 Score =  337 bits (864), Expect = 1e-97
 Identities = 165/240 (68%), Positives = 203/240 (84%)

Query: 1   MILFPAIDLKDGQCVRLVHGLMDQATVFNDDPAAQARAFEEAGFEYIHLVDLNGAFEGKP 60
           MILFPAIDLKDGQCVRL  G M+QATV+N DPAAQARAFEE GFE++H+VDLNGAF G+ 
Sbjct: 1   MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60

Query: 61  VNAAAVESILAAISIPAQLGGGIRDLATIEMWLEKGVRRVIIGTAAVKNPALVIEACRKF 120
           VN AAV++IL A   P QLGGGIR L  IE WL +G++RVI+GT AV++PALVIEACRKF
Sbjct: 61  VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120

Query: 121 PGRIAVGLDAKGGRVATEGWADVSDLTVLDMAGRFEDAGVAAIIYTDIDRDGALQGLNIE 180
           PGR+AVG+DAKGG+VA EGWA+ S+L V+++A +FE AGVAAIIYTDIDRDG L G+N  
Sbjct: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180

Query: 181 ATVSLADAISIPVIASGGLSSIEDLKKLIAANCSGIEGAISGRALYDGRLDPSEALKLLR 240
           +T+ LADA+SIPVIASGGL+S++D++++   +   +EGAISGRALYDGR+DP EAL L+R
Sbjct: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQKLEGAISGRALYDGRIDPKEALDLIR 240


Lambda     K      H
   0.320    0.138    0.395 

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: 283
Number of extensions: 9
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: 243
Length of database: 247
Length adjustment: 24
Effective length of query: 219
Effective length of database: 223
Effective search space:    48837
Effective search space used:    48837
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: 46 (22.3 bits)

Align candidate SMc02570 SMc02570 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))

# 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/TIGR00007.hmm
# target sequence database:        /tmp/gapView.21892.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00007  [M=231]
Accession:   TIGR00007
Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
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-82  260.4   0.1      9e-82  260.2   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc02570  SMc02570 1-(5-phosphoribosyl)-5-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02570  SMc02570 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidaz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.2   0.1     9e-82     9e-82       2     231 .]       4     235 ..       3     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 260.2 bits;  conditional E-value: 9e-82
                           TIGR00007   2 iPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvq 76 
                                         +PaiDlk+G++vrl  Gd+++ tvy+ dp+++a++fee+g+e+lHvVDL+gA++ge++n  ++  i+++++ +vq
  lcl|FitnessBrowser__Smeli:SMc02570   4 FPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGETVNGAAVDAILKATKNPVQ 78 
                                         8************************************************************************** PP

                           TIGR00007  77 vGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvela 151
                                         +GGGiR+le++e++l+ g++rvi+gt+av++p+lv e+ +++   +++v++Dak+g+vav+GW+e sel +vela
  lcl|FitnessBrowser__Smeli:SMc02570  79 LGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKFP-GRVAVGIDAKGGKVAVEGWAEASELGVVELA 152
                                         ******************************************9.******************************* PP

                           TIGR00007 152 kkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk...lgvkgvivGkAlye 223
                                         +k+e +g+++ii+Tdi++dG l+G+n   t el+++++++viasGG +s++d++++++   ++++g+i G+Aly+
  lcl|FitnessBrowser__Smeli:SMc02570 153 RKFEGAGVAAIIYTDIDRDGILTGINWASTLELADAVSIPVIASGGLASMDDIRRMTEpdaQKLEGAISGRALYD 227
                                         *********************************************************98888999********** PP

                           TIGR00007 224 gklklkea 231
                                         g+++ kea
  lcl|FitnessBrowser__Smeli:SMc02570 228 GRIDPKEA 235
                                         ***99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (247 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 7.13
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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