Alignments for a candidate for hisC in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Desulfitobacterium hafniense DCB-2

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_015943472.1 DHAF_RS07450 histidinol-phosphate aminotransferase

Query= curated2:Q24QJ1
         (360 letters)



>NCBI__GCF_000021925.1:WP_015943472.1
          Length = 360

 Score =  679 bits (1751), Expect = 0.0
 Identities = 344/360 (95%), Positives = 350/360 (97%)

Query: 1   MVDKINLEGWMRPSIRTLKAYESKSIPDCVRLDANENPLPWPPGMIEQLLGSDIAFNRYP 60
           MVDK+NLE WMRPSIRTLKAYESKSIPDCVRLDANENPLPWPPGMIEQLLGS IAFNRYP
Sbjct: 1   MVDKMNLEEWMRPSIRTLKAYESKSIPDCVRLDANENPLPWPPGMIEQLLGSAIAFNRYP 60

Query: 61  DGGAQELKEALSRYTGVPAEGILTGNGSDELIQLLMTTFGGEKGAVVIHPPTFSMYEAAA 120
           DGGAQELKEALSRYTGVPAEGILTGNGSDELIQLLMTTFGGEKGAVVIHPPTFSMYEAAA
Sbjct: 61  DGGAQELKEALSRYTGVPAEGILTGNGSDELIQLLMTTFGGEKGAVVIHPPTFSMYEAAA 120

Query: 121 RVTGTGVLEVPLLLTETGRDFRLDVEGMLKAAAQPQVHMIVLCNPNNPTGTLFPREEILR 180
           RVTGT VLEVPLLLTET RDFRLDVEG+LKAAAQPQVHMIVLCNPNNPTGTLFPREEILR
Sbjct: 121 RVTGTEVLEVPLLLTETSRDFRLDVEGILKAAAQPQVHMIVLCNPNNPTGTLFPREEILR 180

Query: 181 IVAESGKIVIVDEAYGEFSGESVVDQIPYCPNLLVMKTFSKLFAMAALRLGYLLGQPSII 240
           IVAESGKIVIVDEAYGEFSGESVVDQIPYCPNLLVMKTFSKLFAMAALRLGYLLGQPSII
Sbjct: 181 IVAESGKIVIVDEAYGEFSGESVVDQIPYCPNLLVMKTFSKLFAMAALRLGYLLGQPSII 240

Query: 241 GALNRARQPFNVNSFSQKAGAIALNYGKEYAEQGRILTAELAKIVEALTAFASVKVFATR 300
           GALNRARQPFNVNSFSQKAG IALNYG+EYAEQGRIL AELA+I EALTAFASVKVFATR
Sbjct: 241 GALNRARQPFNVNSFSQKAGVIALNYGEEYAEQGRILIAELARIAEALTAFASVKVFATR 300

Query: 301 ANFVLFQPEDPDRVYQELIGKGFLIRNMGNLPLVGKALRLSAGSPEDNERLIKALGEILK 360
           ANF+LFQPEDPDRVYQELIGKGFLIR MGNLPLVGKALRLS G PE+NERLIKALGEILK
Sbjct: 301 ANFLLFQPEDPDRVYQELIGKGFLIRTMGNLPLVGKALRLSTGLPEENERLIKALGEILK 360


Lambda     K      H
   0.319    0.138    0.398 

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: 617
Number of extensions: 13
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: 360
Length of database: 360
Length adjustment: 29
Effective length of query: 331
Effective length of database: 331
Effective search space:   109561
Effective search space used:   109561
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: 49 (23.5 bits)

Align candidate WP_015943472.1 DHAF_RS07450 (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.10977.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-100  320.0   0.0   9.2e-100  319.8   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015943472.1  DHAF_RS07450 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015943472.1  DHAF_RS07450 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.8   0.0  9.2e-100  9.2e-100       1     349 []      12     358 ..      12     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.8 bits;  conditional E-value: 9.2e-100
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                               r++i+ l++Y++    + + + v+L++nEnP++ ++ ++e+l  ++  ++rYpd  a+elkeal++y+g
  lcl|NCBI__GCF_000021925.1:WP_015943472.1  12 RPSIRTLKAYES----KSIPDCVRLDANENPLPWPPGMIEQLLGSAIAFNRYPDGGAQELKEALSRYTG 76 
                                               7899********....344469***********************99********************** PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.....gqedl 133
                                               v +e il+gnGsdeli+ll+ +f  ++ av++ +pt+smYe  a+++g+ev evpl        ++ d+
  lcl|NCBI__GCF_000021925.1:WP_015943472.1  77 VPAEGILTGNGSDELIQLLMTTFGGEKGAVVIHPPTFSMYEAAARVTGTEVLEVPLLLTetsrdFRLDV 145
                                               ******************************************************974333356799999 PP

                                 TIGR01141 134 eavle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypn 201
                                               e +l+ aa+ +v+++ l++PnnPtG+l+ reei ++++e+   +V+vDeAY+eFs+e sv++++   pn
  lcl|NCBI__GCF_000021925.1:WP_015943472.1 146 EGILKaAAQPQVHMIVLCNPNNPTGTLFPREEILRIVAES-GKIVIVDEAYGEFSGE-SVVDQIPYCPN 212
                                               9999878899*****************************8.89*************7.*********** PP

                                 TIGR01141 202 lvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkker 270
                                               l+v++T+SK+f++A+lR+Gy++++++ii al++ r+p+nv+s +++a+v al+  ++++++ + +++e 
  lcl|NCBI__GCF_000021925.1:WP_015943472.1 213 LLVMKTFSKLFAMAALRLGYLLGQPSIIGALNRARQPFNVNSFSQKAGVIALNYGEEYAEQGRILIAEL 281
                                               ********************************************************************* PP

                                 TIGR01141 271 erlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreen 339
                                               +r+ e+l+++  ++v+   aNF+l++ + d ++++++l+ kg+++R +++  +l+ ++lR+++G +een
  lcl|NCBI__GCF_000021925.1:WP_015943472.1 282 ARIAEALTAFASVKVFATRANFLLFQPE-DPDRVYQELIGKGFLIRTMGNL-PLVGKALRLSTGLPEEN 348
                                               *************************966.********************99.689************** PP

                                 TIGR01141 340 erllealkei 349
                                               erl++al ei
  lcl|NCBI__GCF_000021925.1:WP_015943472.1 349 ERLIKALGEI 358
                                               *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 7.61
//
[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