Aligments for a candidate for hisC in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Aligments for a candidate for hisC in Desulfovibrio vulgaris Hildenborough

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate 206463 DVU1029 histidinol-phosphate aminotransferase

Query= curated2:Q311Z4
         (383 letters)



>lcl|MicrobesOnline__882:206463 DVU1029 histidinol-phosphate
           aminotransferase
          Length = 373

 Score =  504 bits (1299), Expect = e-147
 Identities = 250/363 (68%), Positives = 291/363 (80%), Gaps = 4/363 (1%)

Query: 19  IRPEVAAFKPYAPGLSIDEIKERYGLSQVVKMASNENPLGTSPLVQQTLRTHADLAFRYV 78
           +RPEV  FKPY PGLSIDEI++R+GL+ VVK+ASNENPLGTSP+VQ+TL+T ADLAFRY 
Sbjct: 12  VRPEVLDFKPYVPGLSIDEIRDRFGLADVVKLASNENPLGTSPVVQRTLKTKADLAFRYA 71

Query: 79  QSGNPRLVSAIARSFGVAAESVVTGNGSDEVIDLIIRVKARPGKHNIVAFNPCFSMYELQ 138
           QSGNPRL  AIA   GVA E VV GNGSDE+IDL+IRV+A PGKHNIVAF PCFS+YELQ
Sbjct: 72  QSGNPRLTRAIAAHHGVAPERVVAGNGSDEIIDLLIRVRATPGKHNIVAFRPCFSIYELQ 131

Query: 139 TRFCGVEFRQVPLRADFSFDYDAFVGAADADTAVAFITTPDNPSGYCPPVEEIIDLARRL 198
            +FCG+EFRQ  LR DF+FD+DAF+ A D +TA+AF+TTPDNPSG+CPPV E+  +AR L
Sbjct: 132 AKFCGLEFRQADLRPDFTFDWDAFLAATDENTAIAFVTTPDNPSGWCPPVSELEHVARTL 191

Query: 199 PSSCLLVVDEAYMDFADDPAAHSVLPHLTEFPNVAVLRTFSKSYGLAGLRLGFGVMHPAL 258
           P SCL V+DEAYMDF  D AAHS+L  L  FPN+AVLRTFSKS+GLAGLRLG+G++   L
Sbjct: 192 PPSCLFVIDEAYMDFCGDEAAHSLLSRLDAFPNIAVLRTFSKSFGLAGLRLGYGILPERL 251

Query: 259 ADYVKRVRLPFSINILAEYAGIAALQDTTFHAQTLRVTREGRTYLTGALTEAGCTVYPSA 318
           ADY+ RVRLPFS+NILAE AG+AAL+DT F ++TLRVT EGR Y+   LT  GC V PS 
Sbjct: 252 ADYLHRVRLPFSVNILAEEAGLAALEDTVFRSETLRVTAEGRAYIAEGLTALGCEVMPSW 311

Query: 319 ANFIMFALPENCPHDARAVFEALLRRGIIIRPLSSYNLPQCLRVSIGNRHENELFIAQFK 378
           ANFIMF      P DA  +FEALLRRGIIIRPL SY LPQ LRVS+GN  EN  FI   K
Sbjct: 312 ANFIMF----RPPTDATDLFEALLRRGIIIRPLKSYGLPQHLRVSVGNADENRRFIEACK 367

Query: 379 ELL 381
           E+L
Sbjct: 368 EIL 370


Lambda     K      H
   0.322    0.137    0.405 

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: 551
Number of extensions: 20
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: 383
Length of database: 373
Length adjustment: 30
Effective length of query: 353
Effective length of database: 343
Effective search space:   121079
Effective search space used:   121079
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 206463 DVU1029 (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.4622.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.7e-101  323.8   0.0   6.4e-101  323.6   0.0    1.0  1  lcl|MicrobesOnline__882:206463  DVU1029 histidinol-phosphate ami


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206463  DVU1029 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.6   0.0  6.4e-101  6.4e-101       1     349 []      13     369 ..      13     369 .. 0.98

  Alignments for each domain:
  == domain 1  score: 323.6 bits;  conditional E-value: 6.4e-101
                       TIGR01141   1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveee 73 
                                     r+++ +++pY+pg       +++g  +vvkL+snEnP+g+s+ v+  lk +++   rY ++ + +l++a+a++ gv +e
  lcl|MicrobesOnline__882:206463  13 RPEVLDFKPYVPGlsideiRDRFGLADVVKLASNENPLGTSPVVQRTLKTKADLAFRYAQSGNPRLTRAIAAHHGVAPE 91 
                                     688999**********9988888888*************************999************************* PP

                       TIGR01141  74 nillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflas 151
                                      +++gnGsde+i+llir  ++pg ++++++ p +s+Ye+ ak++g e ++++l+ d++ d +a+l+a +e++ + f+++
  lcl|MicrobesOnline__882:206463  92 RVVAGNGSDEIIDLLIRVRATPGkHNIVAFRPCFSIYELQAKFCGLEFRQADLRPDFTFDWDAFLAATDENTAIAFVTT 170
                                     ***********************99********************************9********************* PP

                       TIGR01141 152 PnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellaeypnlvvlrTlSKafgLAglRvGyaiana 226
                                     P+nP+G +   +e+e+v+ +   ++l V+DeAY++F+++    s l+ l  +pn++vlrT+SK+fgLAglR+Gy+i  +
  lcl|MicrobesOnline__882:206463 171 PDNPSGWCPPVSELEHVARTLpPSCLFVIDEAYMDFCGDeaaHSLLSRLDAFPNIAVLRTFSKSFGLAGLRLGYGILPE 249
                                     *********************66***************988889999999***************************** PP

                       TIGR01141 227 eiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvkedaeell 305
                                      ++++l++vr p++v+ la ea++aal+d  + ++t++  +++r+++ e+l++l g ev++S+aNF++++ ++da++l+
  lcl|MicrobesOnline__882:206463 250 RLADYLHRVRLPFSVNILAEEAGLAALEDTVFRSETLRVTAEGRAYIAEGLTAL-GCEVMPSWANFIMFRPPTDATDLF 327
                                     ******************************************************.8*********************** PP

                       TIGR01141 306 eallekgiivRdlksaeglleeclRitvGtreenerllealkei 349
                                     eall++gii+R lks+ gl +++lR++vG+++en+r++ea kei
  lcl|MicrobesOnline__882:206463 328 EALLRRGIIIRPLKSY-GL-PQHLRVSVGNADENRRFIEACKEI 369
                                     ****************.85.********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (373 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: 00:00:00.01
# Mc/sec: 8.95
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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