Alignments for a candidate for hisC in Trichlorobacter lovleyi SZ

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Trichlorobacter lovleyi SZ

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012470454.1 GLOV_RS11925 histidinol-phosphate transaminase

Query= curated2:Q2RL44
         (386 letters)



>NCBI__GCF_000020385.1:WP_012470454.1
          Length = 389

 Score =  253 bits (646), Expect = 6e-72
 Identities = 134/356 (37%), Positives = 217/356 (60%), Gaps = 4/356 (1%)

Query: 32  ILSIKPYVPGKPIEEVQRELGVKDVIKLASNENPLGPSPDAVQALQEASDRIFL--YPDG 89
           +   + Y+P  P +E++R  G++ +I+L +NENPLGP P AV AL  + D   +  YP G
Sbjct: 11  VRQFETYIPSPPDDELKRMFGIERLIRLNNNENPLGPPP-AVAALLRSLDPALVPRYPSG 69

Query: 90  NCYYLKEALAAKLGVKQENLIIGNGTDEILKMLAETYINPGDEIVVADPTFSEYEFAAQV 149
           +C++L+E LAA+LG+  + L+ GNG +E++  + + +   GD IV AD TF+ YE+ A+ 
Sbjct: 70  DCFHLREKLAAQLGLTPKQLLFGNGANEVIAFVIKAFCEQGDNIVTADRTFAVYEWIARF 129

Query: 150 MGGRAIKVPTRNFRHDLAAMAAAITPRTRLVFVCNPNNPTGTIVGQAALDGFLKQVPPSV 209
            G  A   P  +F  D  A+ A +  RT+LVF+CNPNNPTG+   +  L  FL+++ P  
Sbjct: 130 SGLEARLAPLNDFGFDEEALLAQVDRRTKLVFICNPNNPTGSWWSRDRLISFLERLGPDH 189

Query: 210 LVVLDEAYSDYVTAEHYPNSLAYVRAGRANVIILRTFSKIYGLAGLRVGYGVAVPEIIRD 269
           LVVLDEAY +++    YP+ ++ + +  +N+II RTFSK+YGLAGLR+GY   V +++  
Sbjct: 190 LVVLDEAYCEFMDQPDYPDGISLL-SRFSNLIIFRTFSKMYGLAGLRIGYLAGVEQVVDS 248

Query: 270 LNRVREPFNVNLLAQVAAVAALKDEAHVGKSREVNSEGKDYLYSQFESLGLKYVPTEANF 329
           + +    ++VN +AQVAA+AA  D+  +  +R +  EG+  L     +L L  +  + NF
Sbjct: 249 IRKTCIVYSVNSIAQVAALAAFGDQEFIRATRSMVREGQQMLAELCSTLQLPLLAGDCNF 308

Query: 330 IFVDIQRDSREVFRQLLQKGVIVRTGDIFGYDTFLRVTIGTRRQNETFIRALREIL 385
             + +       +R L+Q+GV++RT   F +  ++RV+I TR +   F  AL  ++
Sbjct: 309 AMIRLPFSDTLAYRSLMQQGVMIRTMTAFRFPGWIRVSISTRDEMRLFCEALSRLV 364


Lambda     K      H
   0.319    0.137    0.389 

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: 346
Number of extensions: 16
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: 386
Length of database: 389
Length adjustment: 30
Effective length of query: 356
Effective length of database: 359
Effective search space:   127804
Effective search space used:   127804
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: 50 (23.9 bits)

Align candidate WP_012470454.1 GLOV_RS11925 (histidinol-phosphate transaminase)
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.1768863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      5e-94  301.0   0.0    5.6e-94  300.8   0.0    1.0  1  NCBI__GCF_000020385.1:WP_012470454.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020385.1:WP_012470454.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.8   0.0   5.6e-94   5.6e-94       3     348 ..      10     362 ..       8     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 300.8 bits;  conditional E-value: 5.6e-94
                             TIGR01141   3 kikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealaky 67 
                                            ++++e Y p+      +r +g++  ++Ln nEnP+gp++ +++al ++l+   + rYp+ + ++l+e+la++
  NCBI__GCF_000020385.1:WP_012470454.1  10 YVRQFETYIPSppddelKRMFGIERLIRLNNNENPLGPPP-AVAALLRSLDpaLVPRYPSGDCFHLREKLAAQ 81 
                                           58899999998999999999999****************8.66788899997789****************** PP

                             TIGR01141  68 lgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140
                                           lg++++++l+gnG++e+i ++i+af+e+gd++++++ t+++Ye +a++ g e + +pl++ g  d ea+l+++
  NCBI__GCF_000020385.1:WP_012470454.1  82 LGLTPKQLLFGNGANEVIAFVIKAFCEQGDNIVTADRTFAVYEWIARFSGLEARLAPLNDFG-FDEEALLAQV 153
                                           **********************************************************9985.57777777** PP

                             TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFsee...asvlellaeypnlvvlrTlS 209
                                           ++++klvf+++PnnPtG++ +r+ ++ +le+   d lVV+DeAY eF ++   ++ ++ll++++nl++ rT+S
  NCBI__GCF_000020385.1:WP_012470454.1 154 DRRTKLVFICNPNNPTGSWWSRDRLISFLERLGpDHLVVLDEAYCEFMDQpdyPDGISLLSRFSNLIIFRTFS 226
                                           ********************************55****************99999****************** PP

                             TIGR01141 210 KafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleg 282
                                           K++gLAglR+Gy+ + +++++ ++k    y+v+s+a+ aa+aa  d+++i++t   v++++++l e +++l +
  NCBI__GCF_000020385.1:WP_012470454.1 227 KMYGLAGLRIGYLAGVEQVVDSIRKTCIVYSVNSIAQVAALAAFGDQEFIRATRSMVREGQQMLAELCSTL-Q 298
                                           ******************************************************************99999.7 PP

                             TIGR01141 283 levyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                           l    ++ NF +i+++   + ++++l+++g+++R ++++    ++++R+++ tr+e++ + eal++
  NCBI__GCF_000020385.1:WP_012470454.1 299 LPLLAGDCNFAMIRLPFSDTLAYRSLMQQGVMIRTMTAFR--FPGWIRVSISTRDEMRLFCEALSR 362
                                           *************************************994..6*****************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (389 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: 22.73
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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