Aligments for a candidate for hisA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Aligments for a candidate for hisA in Azospirillum brasilense Sp245

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 AZOBR_RS01680 AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= curated2:A7HSH1
         (243 letters)



>FitnessBrowser__azobra:AZOBR_RS01680
          Length = 249

 Score =  320 bits (819), Expect = 2e-92
 Identities = 160/239 (66%), Positives = 191/239 (79%)

Query: 1   MILFPAIDLKDGQCVRLVHGLMDQATVFNDDPAAQARAFEEAGFEYIHLVDLNGAFEGKP 60
           MI++PAIDLKDG CVRL+ G M QATVFN +PA QAR FE  GFE++HLVDLNGAFEGKP
Sbjct: 1   MIIYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKP 60

Query: 61  VNAAAVESILAAISIPAQLGGGIRDLATIEMWLEKGVRRVIIGTAAVKNPALVIEACRKF 120
           VN  AVESIL A++IP QLGGGIRDL TI  WLEKGV RVI+GT A++ P LV EACR+F
Sbjct: 61  VNGKAVESILGAVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREF 120

Query: 121 PGRIAVGLDAKGGRVATEGWADVSDLTVLDMAGRFEDAGVAAIIYTDIDRDGALQGLNIE 180
           PG++AVG+DA+ G VA  GWA+ S +  LD+A +FED+GVAAIIYTDI+RDGA+ G+N+E
Sbjct: 121 PGKVAVGIDAREGYVAVAGWAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVE 180

Query: 181 ATVSLADAISIPVIASGGLSSIEDLKKLIAANCSGIEGAISGRALYDGRLDPSEALKLL 239
           AT  LA  ++ PVIASGG+SSI+DL  L     +GIEG I GRALYDGR+DP  AL LL
Sbjct: 181 ATSDLAFHLTTPVIASGGVSSIDDLIALKKEEDTGIEGVICGRALYDGRIDPKTALDLL 239


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: 269
Number of extensions: 14
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: 243
Length of database: 249
Length adjustment: 24
Effective length of query: 219
Effective length of database: 225
Effective search space:    49275
Effective search space used:    49275
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 AZOBR_RS01680 AZOBR_RS01680 (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.21330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.1e-87  278.6   0.1    2.4e-87  278.4   0.1    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS01680  AZOBR_RS01680 1-(5-phosphoribosy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS01680  AZOBR_RS01680 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneami
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.4   0.1   2.4e-87   2.4e-87       1     230 [.       3     234 ..       3     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 278.4 bits;  conditional E-value: 2.4e-87
                                 TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 
                                               i+PaiDlk+G++vrl++G++++ tv++++p+++a+ fe++g+e+lH+VDL+gA+eg+++n +++++i+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS01680   3 IYPAIDLKDGACVRLLRGEMSQATVFNTEPADQARLFESQGFEWLHLVDLNGAFEGKPVNGKAVESILG 71 
                                               89******************************************************************* PP

                                 TIGR00007  70 elevkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkG 138
                                               +++++vq+GGGiR+l++++++le+gv+rvi+gt+a+++pelv+e+ +e+   k++v++Da+eg vav G
  lcl|FitnessBrowser__azobra:AZOBR_RS01680  72 AVAIPVQLGGGIRDLKTIAHWLEKGVSRVILGTVALREPELVREACREFP-GKVAVGIDAREGYVAVAG 139
                                               *************************************************9.9***************** PP

                                 TIGR00007 139 WkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkal 207
                                               W+e+s++++++la k+e+ g+++ii+Tdi++dG + Gvnve+t++l+ + +++viasGGvssi+d++al
  lcl|FitnessBrowser__azobra:AZOBR_RS01680 140 WAETSTIKALDLALKFEDSGVAAIIYTDINRDGAMGGVNVEATSDLAFHLTTPVIASGGVSSIDDLIAL 208
                                               ********************************************************************* PP

                                 TIGR00007 208 kk...lgvkgvivGkAlyegklklke 230
                                               kk   +g++gvi+G+Aly+g+++ k+
  lcl|FitnessBrowser__azobra:AZOBR_RS01680 209 KKeedTGIEGVICGRALYDGRIDPKT 234
                                               *99999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (249 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.36
//
[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:

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, 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

GapMind for Amino acid biosynthesis