Alignments for a candidate for hisC in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Malonomonas rubra DSM 5091

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_072908153.1 BUB13_RS09200 histidinol-phosphate transaminase

Query= reanno::Marino:GFF2483
         (350 letters)



>NCBI__GCF_900142125.1:WP_072908153.1
          Length = 349

 Score =  231 bits (589), Expect = 2e-65
 Identities = 137/336 (40%), Positives = 201/336 (59%), Gaps = 11/336 (3%)

Query: 9   VNDLVPYVPGEQPKMANLVKLNTNENPFGPSPKVIEAIQAELN---DGLRLYPDPEGESL 65
           + ++  YVPG QP+    +KLNTNENP+ PS KV EAI AEL    + LR YPD   +  
Sbjct: 8   IAEMAGYVPGFQPQEDGWIKLNTNENPYPPSAKVREAIIAELGAEGESLRKYPDAASKEA 67

Query: 66  RETIAAYHKITPEQIFLGNGSDEVLAHIFFGLFQHGEPILFPDITYSFYPVYCGLYNIES 125
           R   A  +K+ PE + + NGSDE+L ++       GE + +   +YS+Y     +   + 
Sbjct: 68  RAVAARLYKVDPEWVIMANGSDELLNNLIRAFAGEGEEVGYIHPSYSYYATLTEIQGAKI 127

Query: 126 KKVPLTESFEINPEDFKQPNGGVIF--PNPNAPTGRYLELQYVEEILAANPNRVVVVDEA 183
           +   LT+ F+I   DF +   G +F   +PNAP G   +  Y+EE LA     V+VVDEA
Sbjct: 128 RTFGLTDDFKI--ADFPERYEGKLFFLTSPNAPLGFIFDNAYIEE-LAQRCAGVLVVDEA 184

Query: 184 YIDFGGESAITLVDKYPNLLVSQTLSKARSLAGLRVGFAVGHPDLIEALNRVKNSFNSYP 243
           Y+DF   SA+ LV K+ N++V++T SK+ SLAG+R+G AV  P++I AL+++++    Y 
Sbjct: 185 YVDFADSSAMQLVKKHENIVVTRTFSKSYSLAGMRLGLAVARPEVIAALDKIRDH---YH 241

Query: 244 LDRLALAGAKAAYEDEAWFRKCCDGVISERERVTAVLEGLGFEVLPSKANFIFARHKEQP 303
           LDRLAL  A AA ED+   R   D V + R+  +  L  LG+EV+PS  NF+FA   ++ 
Sbjct: 242 LDRLALVAATAALEDQEQLRLNVDRVCNVRDCFSNELRKLGYEVIPSHGNFVFAVPSDRD 301

Query: 304 GEVLAKGLREQGIIVRHFNKPRISEFLRITIGTVEQ 339
           G+ +   L E+ I+VR+F+ P +   LRITIGT E+
Sbjct: 302 GKRVYDALFERKILVRYFSDPLLKHGLRITIGTREE 337


Lambda     K      H
   0.319    0.139    0.410 

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: 350
Number of extensions: 21
Number of successful extensions: 5
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: 350
Length of database: 349
Length adjustment: 29
Effective length of query: 321
Effective length of database: 320
Effective search space:   102720
Effective search space used:   102720
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_072908153.1 BUB13_RS09200 (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.16705.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.4e-99  319.2   0.0    1.6e-99  319.1   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072908153.1  BUB13_RS09200 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072908153.1  BUB13_RS09200 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.1   0.0   1.6e-99   1.6e-99       1     349 []       5     348 ..       5     348 .. 0.94

  Alignments for each domain:
  == domain 1  score: 319.1 bits;  conditional E-value: 1.6e-99
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkeala 65 
                                               r++i +++ Y+pg +   e++ +kLn+nEnP++ps kv+ea+ +el     +l++Ypd+ ++e ++ +a
  lcl|NCBI__GCF_900142125.1:WP_072908153.1   5 RKNIAEMAGYVPGFQP-QEDGWIKLNTNENPYPPSAKVREAIIAELGaegeSLRKYPDAASKEARAVAA 72 
                                               789*********9444.44489********************999988888****************** PP

                                 TIGR01141  66 kylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedle 134
                                               + ++v++e ++++nGsdel++ liraf+ +g++v +++p+ys+Y++ ++i+ga++++  l++d+  + +
  lcl|NCBI__GCF_900142125.1:WP_072908153.1  73 RLYKVDPEWVIMANGSDELLNNLIRAFAGEGEEVGYIHPSYSYYATLTEIQGAKIRTFGLTDDF--KIA 139
                                               ***************************************************************4..333 PP

                                 TIGR01141 135 avleaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlv 203
                                               ++   +  + kl fl+sPn+P G +++++ ie+++++   ++ VvDeAY++F+++ s+++l+++++n+v
  lcl|NCBI__GCF_900142125.1:WP_072908153.1 140 DFP--ERYEGKLFFLTSPNAPLGFIFDNAYIEELAQRC-AGVLVVDEAYVDFADS-SAMQLVKKHENIV 204
                                               443..55689***************************9.8999***********6.************* PP

                                 TIGR01141 204 vlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkerer 272
                                               v+rT+SK+++LAg+R+G+a+a +e+i al+k+r+ y++++lal aa+aal+d+++++ +v++v + r+ 
  lcl|NCBI__GCF_900142125.1:WP_072908153.1 205 VTRTFSKSYSLAGMRLGLAVARPEVIAALDKIRDHYHLDRLALVAATAALEDQEQLRLNVDRVCNVRDC 273
                                               ********************************************************************* PP

                                 TIGR01141 273 lleelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreene 340
                                                 +el+kl g ev++S++NFv++  +  d +++++al e++i+vR+++  ++ll++ lRit+Gtree+ 
  lcl|NCBI__GCF_900142125.1:WP_072908153.1 274 FSNELRKL-GYEVIPSHGNFVFAVPSDrDGKRVYDALFERKILVRYFS--DPLLKHGLRITIGTREEMM 339
                                               ********.8***********9854446*******************9..5689*************** PP

                                 TIGR01141 341 rllealkei 349
                                               ++ eal ei
  lcl|NCBI__GCF_900142125.1:WP_072908153.1 340 KIKEALTEI 348
                                               *99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (349 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: 8.88
//
[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