GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1047 Ga0059261_1047 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16)

Query= curated2:Q5NMD5
         (250 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1047 Ga0059261_1047
           1-(5-phosphoribosyl)-5-[(5-
           phosphoribosylamino)methylideneamino]
           imidazole-4-carboxamide isomerase (EC 5.3.1.16)
          Length = 242

 Score =  305 bits (782), Expect = 4e-88
 Identities = 155/239 (64%), Positives = 185/239 (77%), Gaps = 2/239 (0%)

Query: 5   LIIFPAIDLKEGHVVRLSEGDMDRATIYDDDPAARARQFYEAGARYLHVVDLDGAFAGHA 64
           +I+FPAIDLK G VVRL+EGDM RAT+Y ++PAA+A  F +AGA +LHVVDLD AFAG +
Sbjct: 1   VIVFPAIDLKAGQVVRLAEGDMTRATVYGENPAAQAEAFAKAGATHLHVVDLDAAFAGES 60

Query: 65  MNAAAVDAIVKAFPGTIELGGGIRDMNAIDGWLSRGISRVVIGTAAFENPDLVKEAAQKY 124
           +N  AV AI+  FPG ++LGGGIR+  +++ W+  G+SRVVIGTAA E+PD V+EAA  +
Sbjct: 61  INGGAVAAILARFPGKVQLGGGIRNRASVERWIDMGVSRVVIGTAALEDPDFVREAAAAH 120

Query: 125 PGQIVVAVDARDGMVTTKGWAEQSEISVTDMAERFADAGVVALLYTDVGRDGLKKGCNSE 184
           PGQIVVAVDARDG V TKGWA+ S +S+ ++  RF DAGV ALL+TDVGRDGL KGCN E
Sbjct: 121 PGQIVVAVDARDGFVATKGWADVSTVSIAELGHRFEDAGVAALLFTDVGRDGLLKGCNVE 180

Query: 185 ATLALAAATDIPVIASGGVKDIGDIELLARHTKDGIEGVICGRAIYDGSLDLKAALAIA 243
           AT ALAA   IPVIASGGV DI DI  LA   K GIEGVI GRA+YDG LDL  AL  A
Sbjct: 181 ATAALAAEVSIPVIASGGVADISDIHALA--GKPGIEGVITGRALYDGRLDLAEALKAA 237


Lambda     K      H
   0.319    0.136    0.391 

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: 248
Number of extensions: 6
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: 250
Length of database: 242
Length adjustment: 24
Effective length of query: 226
Effective length of database: 218
Effective search space:    49268
Effective search space used:    49268
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: 46 (22.3 bits)

Align candidate Ga0059261_1047 Ga0059261_1047 (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (EC 5.3.1.16))
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.32457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.2e-81  257.4   0.9    7.2e-81  257.2   0.9    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1047  Ga0059261_1047 1-(5-phosphoribos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1047  Ga0059261_1047 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneam
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.2   0.9   7.2e-81   7.2e-81       1     230 [.       3     232 ..       3     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 257.2 bits;  conditional E-value: 7.2e-81
                                 TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 
                                               ++PaiDlk G+vvrl +Gd+++ tvy+++p+++a++f++ ga+ lHvVDLd+A++ge  n  +++ i+ 
  lcl|FitnessBrowser__Korea:Ga0059261_1047   3 VFPAIDLKAGQVVRLAEGDMTRATVYGENPAAQAEAFAKAGATHLHVVDLDAAFAGESINGGAVAAILA 71 
                                               79******************************************************************* PP

                                 TIGR00007  70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138
                                               ++  kvq+GGGiR++++ve+++++gv+rv+igtaa+e+p++v+e++++    +ivv++Da++g va+kG
  lcl|FitnessBrowser__Korea:Ga0059261_1047  72 RFPGKVQLGGGIRNRASVERWIDMGVSRVVIGTAALEDPDFVREAAAAHP-GQIVVAVDARDGFVATKG 139
                                               ********************************************999998.9***************** PP

                                 TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207
                                               W++ s++s++el +++e++g++++++Td+ +dG l+G nve+t  l++e++++viasGGv++i+d++al
  lcl|FitnessBrowser__Korea:Ga0059261_1047 140 WADVSTVSIAELGHRFEDAGVAALLFTDVGRDGLLKGCNVEATAALAAEVSIPVIASGGVADISDIHAL 208
                                               ********************************************************************9 PP

                                 TIGR00007 208 kk.lgvkgvivGkAlyegklklke 230
                                               +   g++gvi G+Aly+g+l+l e
  lcl|FitnessBrowser__Korea:Ga0059261_1047 209 AGkPGIEGVITGRALYDGRLDLAE 232
                                               9758****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (242 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: 6.74
//
[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 preprint 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