Alignments for a candidate for hisC in Desulfovibrio gracilis DSM 16080

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Desulfovibrio gracilis DSM 16080

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_078715991.1 B5D49_RS02160 histidinol-phosphate transaminase

Query= reanno::DvH:206463
         (373 letters)



>NCBI__GCF_900167125.1:WP_078715991.1
          Length = 363

 Score =  397 bits (1019), Expect = e-115
 Identities = 194/359 (54%), Positives = 252/359 (70%)

Query: 12  VRPEVLDFKPYVPGLSIDEIRDRFGLADVVKLASNENPLGTSPVVQRTLKTKADLAFRYA 71
           VR ++LDFKPY PGL++++IR+ +G+  V+KLASNENPLG SPVVQ+ L  KA   FRY 
Sbjct: 5   VRKQILDFKPYTPGLTLEDIREEYGVERVIKLASNENPLGVSPVVQKVLGQKAAEVFRYP 64

Query: 72  QSGNPRLTRAIAAHHGVAPERVVAGNGSDEIIDLLIRVRATPGKHNIVAFRPCFSIYELQ 131
           Q+ +PRL  A+A   GV P+ VV GNGSDEIID+L RV A PG+ N+V +   FS+Y + 
Sbjct: 65  QNHSPRLAAALAERLGVEPDMVVVGNGSDEIIDMLYRVVAEPGRDNVVCYEHSFSMYRMC 124

Query: 132 AKFCGLEFRQADLRPDFTFDWDAFLAATDENTAIAFVTTPDNPSGWCPPVSELEHVARTL 191
           AK CG+E+R+           +    A DE+TA+ F+T+PDNP+G      E+  ++R L
Sbjct: 125 AKLCGVEYREIPREHGLGLPMEHLARAADEHTALVFLTSPDNPTGLAATADEIAKLSRAL 184

Query: 192 PPSCLFVIDEAYMDFCGDEAAHSLLSRLDAFPNIAVLRTFSKSFGLAGLRLGYGILPERL 251
           P   L V+D AY +F   +  +    RL    N+ +LRTFSK++GLAG+RLGYGI+P  L
Sbjct: 185 PEGALLVVDGAYAEFAEPQDIYEAAPRLAELDNLVLLRTFSKAYGLAGMRLGYGIMPAWL 244

Query: 252 ADYLHRVRLPFSVNILAEEAGLAALEDTVFRSETLRVTAEGRAYIAEGLTALGCEVMPSW 311
           A YL R R+PF+VN+ AE AGLAALED VF SETLRV  EGR Y+   L ALGCEV PS 
Sbjct: 245 ASYLRRARIPFTVNLPAEAAGLAALEDEVFLSETLRVVCEGRDYLGRELAALGCEVTPSQ 304

Query: 312 ANFIMFRPPTDATDLFEALLRRGIIIRPLKSYGLPQHLRVSVGNADENRRFIEACKEIL 370
           ANF+MFRPP+DAT  FE +LRRGII+R LKS+GLP H+RV++G   ENR F+ AC+E+L
Sbjct: 305 ANFLMFRPPSDATVFFEGMLRRGIIVRHLKSFGLPDHIRVNMGTESENRAFVSACRELL 363


Lambda     K      H
   0.323    0.139    0.422 

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: 436
Number of extensions: 15
Number of successful extensions: 1
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: 373
Length of database: 363
Length adjustment: 30
Effective length of query: 343
Effective length of database: 333
Effective search space:   114219
Effective search space used:   114219
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_078715991.1 B5D49_RS02160 (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.18465.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-103  332.6   0.0   1.4e-103  332.4   0.0    1.0  1  lcl|NCBI__GCF_900167125.1:WP_078715991.1  B5D49_RS02160 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900167125.1:WP_078715991.1  B5D49_RS02160 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.4   0.0  1.4e-103  1.4e-103       1     348 [.       6     361 ..       6     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 332.4 bits;  conditional E-value: 1.4e-103
                                 TIGR01141   1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkea 63 
                                               r++i +++pY+pg       +e+g + v+kL+snEnP+g+s+ v++ l ++++++ rYp++++ +l +a
  lcl|NCBI__GCF_900167125.1:WP_078715991.1   6 RKQILDFKPYTPGltlediREEYGVERVIKLASNENPLGVSPVVQKVLGQKAAEVFRYPQNHSPRLAAA 74 
                                               78999*************999*********************9999999******************** PP

                                 TIGR01141  64 lakylgveeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqe 131
                                               la++lgve++ +++gnGsde+i++l r ++epg d+v+  e+++smY+++ak++g+e++e+p ++    
  lcl|NCBI__GCF_900167125.1:WP_078715991.1  75 LAERLGVEPDMVVVGNGSDEIIDMLYRVVAEPGrDNVVCYEHSFSMYRMCAKLCGVEYREIPREHGLGL 143
                                               ******************************************************************888 PP

                                 TIGR01141 132 dleavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlell 196
                                                +e+++ aa+e++ lvfl+sP+nPtG   +++ei k+  +  e al VvD AY eF+e    +++++ l
  lcl|NCBI__GCF_900167125.1:WP_078715991.1 144 PMEHLARAADEHTALVFLTSPDNPTGLAATADEIAKLSRALpEGALLVVDGAYAEFAEPqdiYEAAPRL 212
                                               9999999**********************************88**************99889999**** PP

                                 TIGR01141 197 aeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektvee 265
                                               ae +nlv lrT+SKa+gLAg+R+Gy+i+ a ++++l++ r p+ v+ +a +a++aal+d+ ++++t++ 
  lcl|NCBI__GCF_900167125.1:WP_078715991.1 213 AELDNLVLLRTFSKAYGLAGMRLGYGIMPAWLASYLRRARIPFTVNLPAEAAGLAALEDEVFLSETLRV 281
                                               ********************************************************************* PP

                                 TIGR01141 266 vkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvG 334
                                               v ++r++l  el++l g ev +S+aNF++++ ++da+ ++e +l++giivR+lks+ gl ++++R+ +G
  lcl|NCBI__GCF_900167125.1:WP_078715991.1 282 VCEGRDYLGRELAAL-GCEVTPSQANFLMFRPPSDATVFFEGMLRRGIIVRHLKSF-GL-PDHIRVNMG 347
                                               ***************.8***************************************.85.********* PP

                                 TIGR01141 335 treenerllealke 348
                                               t++en++++ a +e
  lcl|NCBI__GCF_900167125.1:WP_078715991.1 348 TESENRAFVSACRE 361
                                               *********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.06
//
[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