Alignments for a candidate for hisC in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Desulfacinum hydrothermale DSM 13146

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_084057874.1 B9A12_RS10615 histidinol-phosphate transaminase

Query= curated2:Q6AQK2
         (379 letters)



>NCBI__GCF_900176285.1:WP_084057874.1
          Length = 396

 Score =  347 bits (889), Expect = e-100
 Identities = 182/364 (50%), Positives = 249/364 (68%), Gaps = 4/364 (1%)

Query: 14  IPENIENIKPYPPGKPLDELEREYGITDSIKLASNENPWGASPKAIKAIGESLGDMQRYP 73
           +P +I  I+PYPPGKP++ELERE GI  SIKLASNENP G SPKA++AI E L  + RYP
Sbjct: 29  VPPHIAAIEPYPPGKPIEELERELGIVGSIKLASNENPLGPSPKALQAIEEKLETLHRYP 88

Query: 74  DGSAYYLTEAIAKYAGVGMSEIILGNGSNEVIEFLVKAFVQDDSEVITSHPSFLMYQKFV 133
           DGS YYL   IA+  GV M  ++LGNGSNE+IE +++ FVQ   EVI  +PSFL+YQ  V
Sbjct: 89  DGSGYYLRNRIAEKFGVPMDGVVLGNGSNEIIELVIRTFVQPGLEVIVPNPSFLVYQLSV 148

Query: 134 QVRGGVNRVIPLKDMHHDLQTILDTVNEKTRLIFIDNPNNPTGTYLEPELLIDFINSLPE 193
           Q  GG    +PL+D+  DL+ IL  + EKTRLIFI+NPNNPTGT L  +    F+  +P+
Sbjct: 149 QCVGGSLVFVPLRDLMIDLEGILKAITEKTRLIFINNPNNPTGTVLPRKNFEAFLEQVPK 208

Query: 194 HVILVLDEAYVDFMDLD-KWLDVPSLIKNQAGRCGIVSLRTFSKAYGLSGLRVGFGLMAE 252
            V++V+DEAY++F D +  +L    L +       +V  RTFSKAYGL+GLRVG+G+M  
Sbjct: 209 DVLVVVDEAYIEFADPNGTFLGFDYLDRRGP---WVVVTRTFSKAYGLAGLRVGYGVMDP 265

Query: 253 EIVTCLHKVRQPFNVNSLAQVGALAALGDVDFYEQTLLKNRQGMKWLMKEIKGLGCEPFA 312
            +   LH+VRQPFNV++ AQ  ALAAL D  F E++    R+ + WL ++++ +G +   
Sbjct: 266 AVADYLHRVRQPFNVSTPAQAAALAALDDEAFLEKSRTLVREQLPWLYQQVQEMGLDFQP 325

Query: 313 SQTNFFLIDVQGNADKLYTEMLYKGVIIRSMSAYGYPHYIRVTVGTTVENKRFLKALSDC 372
           +Q NFFLI +   A  +Y  ML +GVI+R+M++YG P +IR+ VGT  EN+RF++ L   
Sbjct: 326 TQANFFLIRMPVEAKVVYQAMLQEGVIVRAMNSYGLPRHIRINVGTPQENERFIRTLRKV 385

Query: 373 LKEL 376
           LK+L
Sbjct: 386 LKDL 389


Lambda     K      H
   0.320    0.139    0.407 

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: 470
Number of extensions: 13
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: 379
Length of database: 396
Length adjustment: 30
Effective length of query: 349
Effective length of database: 366
Effective search space:   127734
Effective search space used:   127734
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: 50 (23.9 bits)

Align candidate WP_084057874.1 B9A12_RS10615 (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.32702.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-115  370.7   0.0   3.7e-115  370.5   0.0    1.0  1  lcl|NCBI__GCF_900176285.1:WP_084057874.1  B9A12_RS10615 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176285.1:WP_084057874.1  B9A12_RS10615 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.5   0.0  3.7e-115  3.7e-115       2     349 .]      31     385 ..      30     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 370.5 bits;  conditional E-value: 3.7e-115
                                 TIGR01141   2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 
                                               ++i ++epY pg      +relg+ + +kL+snEnP+gps+k+++a++e+l++lhrYpd +++ l++++
  lcl|NCBI__GCF_900176285.1:WP_084057874.1  31 PHIAAIEPYPPGkpieelERELGIVGSIKLASNENPLGPSPKALQAIEEKLETLHRYPDGSGYYLRNRI 99 
                                               57999**************************************************************** PP

                                 TIGR01141  65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133
                                               a+++gv ++ ++lgnGs+e+iel+ir+f++pg +v+v++p++ +Y++s++  g +++ vpl++    dl
  lcl|NCBI__GCF_900176285.1:WP_084057874.1 100 AEKFGVPMDGVVLGNGSNEIIELVIRTFVQPGLEVIVPNPSFLVYQLSVQCVGGSLVFVPLRDL-MIDL 167
                                               **************************************************************99.699* PP

                                 TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellae 198
                                               e +l+a++ek++l+f+ +PnnPtG++l r+++e++le+v +d+lVVvDeAYieF++       +++l +
  lcl|NCBI__GCF_900176285.1:WP_084057874.1 168 EGILKAITEKTRLIFINNPNNPTGTVLPRKNFEAFLEQVpKDVLVVVDEAYIEFADPngtFLGFDYLDR 236
                                               ***************************************88**************98654445677776 PP

                                 TIGR01141 199 y.pnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveev 266
                                               + p +vv+rT+SKa+gLAglRvGy++++++++++l++vr+p+nvs++a++aa+aal+d++++ek+   v
  lcl|NCBI__GCF_900176285.1:WP_084057874.1 237 RgPWVVVTRTFSKAYGLAGLRVGYGVMDPAVADYLHRVRQPFNVSTPAQAAALAALDDEAFLEKSRTLV 305
                                               5379***************************************************************** PP

                                 TIGR01141 267 kkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGt 335
                                               +++  +l+++++++ gl+  + +aNF li+++ +a+ +++a+l++g+ivR ++s+ gl + ++Ri vGt
  lcl|NCBI__GCF_900176285.1:WP_084057874.1 306 REQLPWLYQQVQEM-GLDFQPTQANFFLIRMPVEAKVVYQAMLQEGVIVRAMNSY-GL-PRHIRINVGT 371
                                               **************.8***************************************.85.********** PP

                                 TIGR01141 336 reenerllealkei 349
                                               ++ener+++ l+++
  lcl|NCBI__GCF_900176285.1:WP_084057874.1 372 PQENERFIRTLRKV 385
                                               **********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (396 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.92
//
[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