Alignments for a candidate for hisC in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Sulfurimonas denitrificans DSM 1251

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011372106.1 SUDEN_RS02470 histidinol-phosphate aminotransferase

Query= curated2:A6Q1Z5
         (366 letters)



>NCBI__GCF_000012965.1:WP_011372106.1
          Length = 364

 Score =  454 bits (1168), Expect = e-132
 Identities = 221/359 (61%), Positives = 283/359 (78%), Gaps = 1/359 (0%)

Query: 1   MRFNETLEKIKTYEAGKPIELVVREFGIEPQNIIKLASNENPYGTSPKVVDAVREIADTM 60
           M+FN+ L+ IKTYEAGKPIELVVRE+GIEPQ+I+KLASNENP G SPKV+DAV +I   M
Sbjct: 1   MKFNKHLQNIKTYEAGKPIELVVREYGIEPQDIVKLASNENPLGCSPKVIDAVGKILTKM 60

Query: 61  YMYPDDSMFELKSALAKRFEIDQKNIIIGAGSDQVLEFCARAVLNEKSSVLMSKITFAMY 120
            +YPDDSM  LK+AL+KR+ +D +N+IIG+GSDQV+EF   A  +  S +LM+ ITFAMY
Sbjct: 61  SLYPDDSMISLKNALSKRYNVDSENVIIGSGSDQVIEFLIHAKAHSGSKILMNSITFAMY 120

Query: 121 EIYALQQGAKIIRSSCYRHDLEEFYDLYKKHHPDIIHICTPNNPTGDALDAEYLYSFLDN 180
           EIY+   GA +IR+S   HDL+EFY+LYK+  P+II ICTPNNPTGDALDA+ +Y+FL+ 
Sbjct: 121 EIYSKHVGADVIRTSSQEHDLDEFYELYKQEKPEIIFICTPNNPTGDALDAQKIYNFLEK 180

Query: 181 V-QEPLVIVDGAYMEYAAFKDEKKRIHPQDLIKKYPNVIYLGTFSKAYGLGGMRVGYGIA 239
           +  + LV+VD AYMEYA  KD KK I+ ++LI+K+ NVIYLGTFSKAYGLGGMRVGYGI+
Sbjct: 181 IDNDTLVVVDAAYMEYAIVKDAKKEINVKELIQKHSNVIYLGTFSKAYGLGGMRVGYGIS 240

Query: 240 DQSVIGQLYKLRPPFNITTLSLKAATTALEDEGFVQYSIEQNFLQMERFVNFALQNGFEF 299
           +  +I +LYKLRPPFNITTLSL+AAT AL DE FVQ S   N  QM+R+  FA +   + 
Sbjct: 241 EAKIIKELYKLRPPFNITTLSLEAATVALSDEEFVQKSTALNLEQMKRYEEFAKEQKIDI 300

Query: 300 IDSYTNFITYLLPENRKSKSLSEALLKRGVIVRDLTGYGMNALRITVGTKEQNDRFFEI 358
           I+SYTNF+T  L  N+ S  ++  LL+ G+IVRDL+ Y MNA+R+T+GT+EQN RFF++
Sbjct: 301 INSYTNFVTLSLGSNQNSTKIASQLLQNGMIVRDLSSYNMNAIRVTIGTQEQNSRFFKL 359


Lambda     K      H
   0.320    0.138    0.393 

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: 487
Number of extensions: 19
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: 366
Length of database: 364
Length adjustment: 30
Effective length of query: 336
Effective length of database: 334
Effective search space:   112224
Effective search space used:   112224
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: 49 (23.5 bits)

Align candidate WP_011372106.1 SUDEN_RS02470 (histidinol-phosphate aminotransferase)
to HMM TIGR01141 (hisC: histidinol-phosphate transaminase (EC 2.6.1.9))

# 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/TIGR01141.hmm
# target sequence database:        /tmp/gapView.10266.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01141  [M=349]
Accession:   TIGR01141
Description: hisC: histidinol-phosphate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-107  345.7   4.0   1.5e-107  345.5   4.0    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011372106.1  SUDEN_RS02470 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011372106.1  SUDEN_RS02470 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.5   4.0  1.5e-107  1.5e-107       2     345 ..       5     359 ..       4     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 345.5 bits;  conditional E-value: 1.5e-107
                                 TIGR01141   2 ekikklepYqpg......arelgek..evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelke 62 
                                               +++++++ Y++g       re+g++  ++vkL+snEnP+g+s+kv++a+ + l+k+ +Ypd++++ lk+
  lcl|NCBI__GCF_000012965.1:WP_011372106.1   5 KHLQNIKTYEAGkpielvVREYGIEpqDIVKLASNENPLGCSPKVIDAVGKILTKMSLYPDDSMISLKN 73 
                                               789***************9*****999****************************************** PP

                                 TIGR01141  63 alakylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqe 131
                                               al+k+++v+ en+++g Gsd++ie+li+a +++g ++l+++ t++mYe+++k  ga+v+ ++ +e+  +
  lcl|NCBI__GCF_000012965.1:WP_011372106.1  74 ALSKRYNVDSENVIIGSGSDQVIEFLIHAKAHSGSKILMNSITFAMYEIYSKHVGADVIRTSSQEHDLD 142
                                               ***************************************************************999656 PP

                                 TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee......asvl 193
                                               ++ +++  ++ek++++f+++PnnPtG  l++++i ++le+  +d+lVVvD AY+e++         +v 
  lcl|NCBI__GCF_000012965.1:WP_011372106.1 143 EFYELY--KQEKPEIIFICTPNNPTGDALDAQKIYNFLEKIdNDTLVVVDAAYMEYAIVkdakkeINVK 209
                                               655555..99*******************************77*************9777788888999 PP

                                 TIGR01141 194 ellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiekt 262
                                               el+++++n+++l T+SKa+gL+g+RvGy+i++a+ii++l k+r+p+n+++l+leaa+ al+d+++++k+
  lcl|NCBI__GCF_000012965.1:WP_011372106.1 210 ELIQKHSNVIYLGTFSKAYGLGGMRVGYGISEAKIIKELYKLRPPFNITTLSLEAATVALSDEEFVQKS 278
                                               ********************************************************************* PP

                                 TIGR01141 263 veevkkererlleelkkleglevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleecl 329
                                               ++ + ++++r++e++k+  ++++++S++NFv++ + +  ++++++ +ll++g+ivRdl+s+ ++  +++
  lcl|NCBI__GCF_000012965.1:WP_011372106.1 279 TALNLEQMKRYEEFAKEQ-KIDIINSYTNFVTLSLGSnqNSTKIASQLLQNGMIVRDLSSY-NM--NAI 343
                                               **************9999.7*************997777999*****************99.55..*** PP

                                 TIGR01141 330 RitvGtreenerllea 345
                                               R+t+Gt+e+n r+++ 
  lcl|NCBI__GCF_000012965.1:WP_011372106.1 344 RVTIGTQEQNSRFFKL 359
                                               *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (364 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.95
//
[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