Alignments for a candidate for hisA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisA in Dinoroseobacter shibae DFL-12

Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate 3609192 Dshi_2578 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (RefSeq)

Query= reanno::Smeli:SMc02570
         (247 letters)



>FitnessBrowser__Dino:3609192
          Length = 240

 Score =  297 bits (760), Expect = 1e-85
 Identities = 155/241 (64%), Positives = 185/241 (76%), Gaps = 1/241 (0%)

Query: 1   MILFPAIDLKDGQCVRLKLGDMEQATVYNPDPAAQARAFEEQGFEWLHVVDLNGAFAGET 60
           MIL+PAIDLKDGQ VRL  GDM++ATV+N  PAAQARAF++ G  WLH+VDLNGAFAG  
Sbjct: 1   MILYPAIDLKDGQAVRLYKGDMDKATVFNDSPAAQARAFQDAGCAWLHLVDLNGAFAGAP 60

Query: 61  VNGAAVDAILKATKNPVQLGGGIRTLEHIENWLSRGLKRVILGTVAVRDPALVIEACRKF 120
           VN AAV+AIL  T  P QLGGGIR +  IE WL +G+ RVILGTVAV DP LV  A + F
Sbjct: 61  VNAAAVEAILAETSVPAQLGGGIRDMATIEMWLGKGIARVILGTVAVEDPELVRAAAKAF 120

Query: 121 PGRVAVGIDAKGGKVAVEGWAEASELGVVELARKFEGAGVAAIIYTDIDRDGILTGINWA 180
           PG+VAVG+DA+ G+VA  GWAE ++L V +LAR FE AGVAAIIYTDIDRDG + G N A
Sbjct: 121 PGQVAVGLDARAGRVATRGWAEETDLMVTDLARSFEDAGVAAIIYTDIDRDGAMQGPNVA 180

Query: 181 STLELADAVSIPVIASGGLASMDDIRRMTEPDAQKLEGAISGRALYDGRIDPKEALDLIR 240
           +T  LA A SIPVIASGG++S+DD+R +    A  L+GAISGRALYDG ID  EAL ++ 
Sbjct: 181 ATAALARATSIPVIASGGVSSLDDLRALKASGA-PLDGAISGRALYDGAIDLAEALAVLA 239

Query: 241 E 241
           +
Sbjct: 240 D 240


Lambda     K      H
   0.319    0.138    0.401 

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: 258
Number of extensions: 11
Number of successful extensions: 4
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: 247
Length of database: 240
Length adjustment: 23
Effective length of query: 224
Effective length of database: 217
Effective search space:    48608
Effective search space used:    48608
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 3609192 Dshi_2578 (phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (RefSeq))
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.6566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.8e-82  262.4   0.0    2.1e-82  262.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609192  Dshi_2578 phosphoribosylformimin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609192  Dshi_2578 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.2   0.0   2.1e-82   2.1e-82       1     230 [.       3     233 ..       3     234 .. 0.98

  Alignments for each domain:
  == domain 1  score: 262.2 bits;  conditional E-value: 2.1e-82
                         TIGR00007   1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkiveelevkvqv 77 
                                       ++PaiDlk+G++vrl++Gd+dk tv++d+p+++a++f++ g  +lH+VDL+gA++g+++n+ +++ i+ e++v+ q+
  lcl|FitnessBrowser__Dino:3609192   3 LYPAIDLKDGQAVRLYKGDMDKATVFNDSPAAQARAFQDAGCAWLHLVDLNGAFAGAPVNAAAVEAILAETSVPAQL 79 
                                       59*************************************************************************** PP

                         TIGR00007  78 GGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevavkGWkekselslvelakkl 154
                                       GGGiR+++++e +l +g++rvi+gt+ave+pelv+ ++k++   +++v+lDa+ g+va++GW+e+++l +++la+ +
  lcl|FitnessBrowser__Dino:3609192  80 GGGIRDMATIEMWLGKGIARVILGTVAVEDPELVRAAAKAFP-GQVAVGLDARAGRVATRGWAEETDLMVTDLARSF 155
                                       *****************************************9.99******************************** PP

                         TIGR00007 155 eelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvkalkk..lgvkgvivGkAlyegklklk 229
                                       e++g+++ii+Tdi++dG ++G+nv +t  l+++++++viasGGvss +d++alk+  + ++g+i G+Aly+g ++l 
  lcl|FitnessBrowser__Dino:3609192 156 EDAGVAAIIYTDIDRDGAMQGPNVAATAALARATSIPVIASGGVSSLDDLRALKAsgAPLDGAISGRALYDGAIDLA 232
                                       ******************************************************9444479*************998 PP

                         TIGR00007 230 e 230
                                       e
  lcl|FitnessBrowser__Dino:3609192 233 E 233
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (231 nodes)
Target sequences:                          1  (240 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: 6.34
//
[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