Alignments for a candidate for hisC in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Heliobacterium modesticaldum Ice1; ATCC 51547

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012284031.1 HM1_RS13875 histidinol-phosphate transaminase

Query= curated2:Q24QJ1
         (360 letters)



>NCBI__GCF_000019165.1:WP_012284031.1
          Length = 418

 Score =  296 bits (759), Expect = 5e-85
 Identities = 166/358 (46%), Positives = 229/358 (63%), Gaps = 16/358 (4%)

Query: 10  WMRPSIRTLKAYESKSIPDCVRLDANENPLPWPPGMIEQLLGSDIA---FNRYPDGGAQE 66
           W+R  IR +  Y++K  P+ V++DANENP PWP   +E+L   D+A   F+RYPDG A++
Sbjct: 7   WVRQDIRHIVPYQAKVYPEGVKVDANENPFPWPASYVEKLQ-KDLAAYPFSRYPDGEAKD 65

Query: 67  LKEALSRYTGVPAEGILTGNGSDELIQLLMTTFGGEKGAVVIHPPTFSMYEAAARVTGTG 126
           L++ALS YTG     IL  NGSDE IQL++ TFGG   A VI  PTF MY  A R  G  
Sbjct: 66  LRQALSAYTGRDPAEILISNGSDEAIQLILLTFGGPGLATVISNPTFVMYAMATRYMGGQ 125

Query: 127 VLEVPLLLTETGRDFRLDVEGMLKAAAQPQVHMIVLCNPNNPTGTLFPREEILRIVAESG 186
           V++VPLL  E    FRLDVEG+L AA++ +  +I++CNPNNPTG  F  E+I+ ++  + 
Sbjct: 126 VIDVPLL--EEAGTFRLDVEGLLSAASREESRVIIICNPNNPTGNSFAEEDIVAVLRGTD 183

Query: 187 KIVIVDEAYGEFSGESVVDQIPYCPNLLVMKTFSKLFAMAALRLGYLLGQPSIIGALNRA 246
           KIVIVDEAY EF G+S+V +I   PNL+VM+TFSK FA+A LR+GY +   +II  +++ 
Sbjct: 184 KIVIVDEAYYEFYGKSMVGRIGEFPNLIVMRTFSKAFALAGLRVGYTMASRAIINEIHKV 243

Query: 247 RQPFNVNSFSQKAGAIALNYGKEYAEQGRILTAELAKIVEALTAFASVKVFATRANFVL- 305
           RQPFNVN+FSQ++ AIAL     +  Q + + AE   ++  L  F    VF T AN+V  
Sbjct: 244 RQPFNVNAFSQRSAAIALEERAAFENQVKTILAERETLLPQLKRF-DWDVFPTDANYVFL 302

Query: 306 -FQPEDP-------DRVYQELIGKGFLIRNMGNLPLVGKALRLSAGSPEDNERLIKAL 355
             + E P         +++ L+ +G LIR +G  P +   LR++ G PE+N RLI AL
Sbjct: 303 RLRGESPAARAALAASIHKALMDRGVLIRKLGGGPSLDGTLRITVGQPEENRRLIVAL 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: 399
Number of extensions: 17
Number of successful extensions: 4
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: 418
Length adjustment: 30
Effective length of query: 330
Effective length of database: 388
Effective search space:   128040
Effective search space used:   128040
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_012284031.1 HM1_RS13875 (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.16106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-104  334.5   0.0   3.8e-104  334.3   0.0    1.0  1  lcl|NCBI__GCF_000019165.1:WP_012284031.1  HM1_RS13875 histidinol-phosphate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012284031.1  HM1_RS13875 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.3   0.0  3.8e-104  3.8e-104       1     348 [.       9     362 ..       9     363 .. 0.96

  Alignments for each domain:
  == domain 1  score: 334.3 bits;  conditional E-value: 3.8e-104
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealaky 67 
                                               r++i+++ pYq+  +     e vk ++nEnPf+ + + +e+l++ l+  ++ rYpd +a++l++al++y
  lcl|NCBI__GCF_000019165.1:WP_012284031.1   9 RQDIRHIVPYQA--K--VYPEGVKVDANENPFPWPASYVEKLQKDLAayPFSRYPDGEAKDLRQALSAY 73 
                                               799*********..3..33369************************9999******************* PP

                                 TIGR01141  68 lgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked...gqedl 133
                                               +g ++++il++nGsde+i+l++ +f  pg a+++++pt+ mY++ ++  g +v+ vpl e+   ++ d+
  lcl|NCBI__GCF_000019165.1:WP_012284031.1  74 TGRDPAEILISNGSDEAIQLILLTFGGPGLATVISNPTFVMYAMATRYMGGQVIDVPLLEEagtFRLDV 142
                                               **********************************************************99999999999 PP

                                 TIGR01141 134 eavle.aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypn 201
                                               e +l  a  e+ +++ +++PnnPtGn++ +e+i++vl  + d +V+vDeAY+eF ++ s++  + e+pn
  lcl|NCBI__GCF_000019165.1:WP_012284031.1 143 EGLLSaASREESRVIIICNPNNPTGNSFAEEDIVAVLRGT-DKIVIVDEAYYEFYGK-SMVGRIGEFPN 209
                                               999886888999***************************9.9**************7.*********** PP

                                 TIGR01141 202 lvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkker 270
                                               l+v+rT+SKaf+LAglRvGy++a+ +ii++++kvr+p+nv+  ++  a  al++++ +e++v+ + +er
  lcl|NCBI__GCF_000019165.1:WP_012284031.1 210 LIVMRTFSKAFALAGLRVGYTMASRAIINEIHKVRQPFNVNAFSQRSAAIALEERAAFENQVKTILAER 278
                                               ********************************************************************* PP

                                 TIGR01141 271 erlleelkkleglevyeSkaNFvlikvke........daeelleallekgiivRdlksaeglleeclRi 331
                                               e ll +lk + + +v++ +aN+v+++++          a+ + +al+++g+++R+l+  ++ l++ lRi
  lcl|NCBI__GCF_000019165.1:WP_012284031.1 279 ETLLPQLKRF-DWDVFPTDANYVFLRLRGespaaraaLAASIHKALMDRGVLIRKLGGGPS-LDGTLRI 345
                                               **********.69**************99999887666778899**************987.6****** PP

                                 TIGR01141 332 tvGtreenerllealke 348
                                               tvG++een+rl+ al++
  lcl|NCBI__GCF_000019165.1:WP_012284031.1 346 TVGQPEENRRLIVALEK 362
                                               *************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (418 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: 11.67
//
[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