Alignments for a candidate for hisN in Chlorobium phaeobacteroides BS1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Chlorobium phaeobacteroides BS1

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_012474362.1 CPHAMN1_RS04615 histidinol-phosphatase

Query= curated2:P56160
         (259 letters)



>NCBI__GCF_000020545.1:WP_012474362.1
          Length = 252

 Score =  362 bits (928), Expect = e-105
 Identities = 177/249 (71%), Positives = 206/249 (82%), Gaps = 1/249 (0%)

Query: 1   MTPDLQLALELAEKAGKLTLDYFGRRSLQVFSKRDDTPVTEADRNAEELIRQGISAKFPD 60
           MT D+QLA++LA  AG L L Y+  +SL++ SKRDDTPVTEADR AE LIR+GI+  FPD
Sbjct: 1   MTDDMQLAVKLARDAGTLILSYYRSKSLKIDSKRDDTPVTEADRKAESLIRKGITEVFPD 60

Query: 61  DGLFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPALG 120
           DG+FGEEFDE  S NGRRWI+DPIDGTRSFIHGVPL+GVMI LEV+  M++G +NFPALG
Sbjct: 61  DGIFGEEFDEKLSVNGRRWILDPIDGTRSFIHGVPLFGVMIGLEVDREMRVGAVNFPALG 120

Query: 121 ELYQAERGSGAFMNGSPVQVSAIAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAGLVRG 180
           E+Y AE GSGAF NG  + VSAI++   +TVVFTEKEYLLDP S+HPVD LR DAGLVRG
Sbjct: 121 EIYYAETGSGAFFNGEAISVSAISDYREATVVFTEKEYLLDPLSDHPVDSLRHDAGLVRG 180

Query: 181 WGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEGLVSA 240
           WGDCYGHMLVASGRAEVAVDKIMSPWDCAA+IP+V EAGG CFDY G ++ I G+GLVS 
Sbjct: 181 WGDCYGHMLVASGRAEVAVDKIMSPWDCAALIPVVTEAGGRCFDYTG-ETTIYGQGLVST 239

Query: 241 NNAMGRNLI 249
           N  +G  L+
Sbjct: 240 NRFIGDKLL 248


Lambda     K      H
   0.319    0.138    0.415 

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: 271
Number of extensions: 5
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: 259
Length of database: 252
Length adjustment: 24
Effective length of query: 235
Effective length of database: 228
Effective search space:    53580
Effective search space used:    53580
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: 47 (22.7 bits)

Align candidate WP_012474362.1 CPHAMN1_RS04615 (histidinol-phosphatase)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))

# 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/TIGR02067.hmm
# target sequence database:        /tmp/gapView.24063.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02067  [M=252]
Accession:   TIGR02067
Description: his_9_HisN: histidinol-phosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.3e-89  285.2   0.0    2.6e-89  285.0   0.0    1.0  1  lcl|NCBI__GCF_000020545.1:WP_012474362.1  CPHAMN1_RS04615 histidinol-phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020545.1:WP_012474362.1  CPHAMN1_RS04615 histidinol-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.0   0.0   2.6e-89   2.6e-89       2     248 ..       5     248 ..       4     252 .] 0.97

  Alignments for each domain:
  == domain 1  score: 285.0 bits;  conditional E-value: 2.6e-89
                                 TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdktpVteADraaEeaireliaakfPddgilGEEfgeeee 70 
                                               ++la +la+ ag  il+y+r ++lk d+k+d+tpVteADr+aE++ir+ i++ fPddgi+GEEf+e+ +
  lcl|NCBI__GCF_000020545.1:WP_012474362.1   5 MQLAVKLARDAGTLILSYYRSKSLKIDSKRDDTPVTEADRKAESLIRKGITEVFPDDGIFGEEFDEKLS 73 
                                               6899***************************************************************** PP

                                 TIGR02067  71 daeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallnggerelrv 139
                                                ++++W+lDPiDGT+sFi+GvP++g++i+L+ + ++ +G +++Palge+++a++g+ga+ ng  + ++v
  lcl|NCBI__GCF_000020545.1:WP_012474362.1  74 VNGRRWILDPIDGTRSFIHGVPLFGVMIGLEVDREMRVGAVNFPALGEIYYAETGSGAFFNG--EAISV 140
                                               *************************************************************7..8**** PP

                                 TIGR02067 140 sevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDia 208
                                               s++++  +A++v+t++++l d+ + + +++lr++a l+r++gdcy+++lvAsGr++++v++++sp+D+a
  lcl|NCBI__GCF_000020545.1:WP_012474362.1 141 SAISDYREATVVFTEKEYLLDPLSDHPVDSLRHDAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCA 209
                                               ********************************************************************* PP

                                 TIGR02067 209 alipiieeAggvitdwkGkeaeeggeavaaanaalhdevl 248
                                               alip+++eAgg ++d++G+++  g    +++n+ + d++l
  lcl|NCBI__GCF_000020545.1:WP_012474362.1 210 ALIPVVTEAGGRCFDYTGETTIYGQGL-VSTNRFIGDKLL 248
                                               ******************998876555.999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (252 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: 8.81
//
[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:

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