Alignments for a candidate for hisC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Dinoroseobacter shibae DFL-12

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate 3609562 Dshi_2946 histidinol-phosphate aminotransferase (RefSeq)

Query= reanno::Phaeo:GFF2492
         (361 letters)



>FitnessBrowser__Dino:3609562
          Length = 361

 Score =  555 bits (1431), Expect = e-163
 Identities = 277/357 (77%), Positives = 303/357 (84%)

Query: 1   MTHIAPQPGILDIALYEGGAAHVKGMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYP 60
           MT I PQPGI+DIALYEGGA+ V G+  V KLSSNENPLGPSP AI A +AA  E+HRYP
Sbjct: 1   MTQITPQPGIMDIALYEGGASKVDGLDTVIKLSSNENPLGPSPAAIAAYKAAAGELHRYP 60

Query: 61  SSDHSGLRQAIGEVYGLPMEQIICGAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISA 120
           S+DH+GLR AI EVYGL  E+IICGAGSDEII FLCQAY GPGDEV+ TEHGFAMYRIS 
Sbjct: 61  STDHAGLRGAIAEVYGLDPERIICGAGSDEIIAFLCQAYVGPGDEVIHTEHGFAMYRIST 120

Query: 121 LAAGATPVEVAERDRVTDVDALLAGCTERTRLVFIANPNNPTGTMIGMADLARLADGLPK 180
           LAAG TPVEV ER+RVTDVDA+LAG T+RTRLVFIANPNNPTGTMIG   LARLADGLP+
Sbjct: 121 LAAGGTPVEVPERERVTDVDAILAGVTDRTRLVFIANPNNPTGTMIGGNALARLADGLPE 180

Query: 181 GALLVLDGAYAEYVEGYDAGAALVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVL 240
           G LLVLDGAYAEYV  YDAG ALV +R+NVVMTRTFSKIYGLG  RVGWGY P+ +IDVL
Sbjct: 181 GCLLVLDGAYAEYVPDYDAGKALVESRENVVMTRTFSKIYGLGALRVGWGYGPRHVIDVL 240

Query: 241 NRVRGPFNLSSTALAGAEAAVRDTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFI 300
           NRVRGPFNLS+ ALA AEAAVRD  YTE CR ENAKWR WLA  LA LG+PSDTS ANF+
Sbjct: 241 NRVRGPFNLSTGALAAAEAAVRDRAYTETCRAENAKWRGWLASELAALGIPSDTSSANFV 300

Query: 301 LARFASPEEAGACDAFLQSRGLIVRRVTGYKLPAALRITVGDETACNALVAAMKVFK 357
           LARFASPEEAGACD FL++RG+IVRRV+GYKLPAALR+TVGD   C ALV A+  FK
Sbjct: 301 LARFASPEEAGACDDFLKARGIIVRRVSGYKLPAALRMTVGDAEGCRALVDAVAAFK 357


Lambda     K      H
   0.318    0.134    0.399 

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: 506
Number of extensions: 11
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: 361
Length of database: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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 3609562 Dshi_2946 (histidinol-phosphate aminotransferase (RefSeq))
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.29150.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    3.7e-95  304.7   0.0    4.2e-95  304.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609562  Dshi_2946 histidinol-phosphate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609562  Dshi_2946 histidinol-phosphate aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.5   0.0   4.2e-95   4.2e-95       3     347 ..       9     354 ..       7     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 304.5 bits;  conditional E-value: 4.2e-95
                         TIGR01141   3 kikklepYqpgare.lgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeenillg 78 
                                        i +++ Y+ ga++ +g + v+kL+snEnP+gps+++++a+k+++ +lhrYp+ +++ l+ a+a+++g+++e i+ g
  lcl|FitnessBrowser__Dino:3609562   9 GIMDIALYEGGASKvDGLDTVIKLSSNENPLGPSPAAIAAYKAAAGELHRYPSTDHAGLRGAIAEVYGLDPERIICG 85 
                                       6888999999965516778********************************************************** PP

                         TIGR01141  79 nGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklvflasPnnP 155
                                       +Gsde+i +l++a++ pgd+v+ +e+ ++mY++s+ +ag   +evp +e    d++a+l+ ++++++lvf+a+PnnP
  lcl|FitnessBrowser__Dino:3609562  86 AGSDEIIAFLCQAYVGPGDEVIHTEHGFAMYRISTLAAGGTPVEVPERER-VTDVDAILAGVTDRTRLVFIANPNNP 161
                                       ***********************************************999.69************************ PP

                         TIGR01141 156 tGnllkreeiekvleev.edalVVvDeAYieFseeasv.lellaeypnlvvlrTlSKafgLAglRvGyaianaeiie 230
                                       tG+++  + + ++++   e +l V+D AY e+ +++++   l++ ++n+v++rT+SK++gL++lRvG +++  ++i+
  lcl|FitnessBrowser__Dino:3609562 162 TGTMIGGNALARLADGLpEGCLLVLDGAYAEYVPDYDAgKALVESRENVVMTRTFSKIYGLGALRVGWGYGPRHVID 238
                                       *****************88****************77615688999******************************* PP

                         TIGR01141 231 alekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkkleglevyeSkaNFvlikvke..daeell 305
                                       +l++vr p+n+s+ al+aa aa+rd++++e + +e++k r +l +el++l g+    S aNFvl+++ +  +a ++ 
  lcl|FitnessBrowser__Dino:3609562 239 VLNRVRGPFNLSTGALAAAEAAVRDRAYTETCRAENAKWRGWLASELAAL-GIPSDTSSANFVLARFASpeEAGACD 314
                                       **************************************************.8***************9987788888 PP

                         TIGR01141 306 eallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                       + l+ +giivR ++ ++  l+ +lR+tvG +e +++l++a++
  lcl|FitnessBrowser__Dino:3609562 315 DFLKARGIIVRRVSGYK--LPAALRMTVGDAEGCRALVDAVA 354
                                       89999***********4..6*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (361 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: 11.24
//
[ok]

This GapMind analysis is from Apr 09 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