Alignments for a candidate for hisC in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Sphingomonas koreensis DSMZ 15582

Align Histidinol-phosphate aminotransferase; Imidazole acetol phosphate aminotransferase; IAP aminotransferase; Imidazole acetol-phosphate transaminase; EC 2.6.1.9 (characterized)
to candidate Ga0059261_2299 Ga0059261_2299 histidinol-phosphate aminotransferase

Query= SwissProt::P34037
         (369 letters)



>FitnessBrowser__Korea:Ga0059261_2299
          Length = 376

 Score =  462 bits (1190), Expect = e-135
 Identities = 222/360 (61%), Positives = 276/360 (76%)

Query: 8   RPKSWIDSIAPYIPGSSKTLDGRPAVKLSSNENPLGTSLKAKEAYREAIDSLSLYPDSGA 67
           +PK WI  IAPY+PG SKT DGR A+KLSSNENPLGTS KA+ A+  A +SL  YPD+ A
Sbjct: 9   QPKPWIMDIAPYVPGKSKTDDGRKAIKLSSNENPLGTSDKARAAFATAANSLERYPDASA 68

Query: 68  TALREAIGACYNLDPARIIHGTGSDEILHLAAGAYAGQDDEVLYPRYSFSVYPLAARRVG 127
             LREA+   + LD ARII+G GSDE+LHLAAGA+AG  DE++Y  Y F+VYP+A +RVG
Sbjct: 69  VELREALAELHGLDAARIIYGNGSDEVLHLAAGAFAGPGDEIIYVNYGFTVYPIATKRVG 128

Query: 128 ATPVEAPDDDYRCSVDALLKAVTPRTRVVFIANPNNPTGTWITRAEVEKLHNGLPRNCLL 187
           ATPV A D DY   VDA+L +VT RTR+VF+ANPNNPTGT+ +R E+ +LH GL  + LL
Sbjct: 129 ATPVVAADADYATDVDAILASVTDRTRIVFVANPNNPTGTYASREEIARLHAGLRPDILL 188

Query: 188 VIDQAYAEYLDPECDDGALALAKNTKNVLVTRTFSKIYGLAAERIGWAYACPEIIDALNR 247
           V+D AYAEY++ E DDG + LAK   NVLVTRTFSK+YGLAAERIGW Y   E+I+A++R
Sbjct: 189 VLDHAYAEYIEGEIDDGGMELAKTQPNVLVTRTFSKLYGLAAERIGWGYGSAEVIEAMHR 248

Query: 248 IRAPFNVTIAGQKAAVAALEDQAFIQNSFKHNKKWRGWFENQMALLSNAGIRVIPSSANF 307
           IR PF++TIAG  AA+AAL D AF++++  HN +WR WF +++A L NAG+R +PS ANF
Sbjct: 249 IRLPFSITIAGTAAAIAALHDSAFVEHTRSHNAQWRRWFADEIAKLGNAGLRAVPSQANF 308

Query: 308 TLLLFEGSLTAETAYKALMDHGYTTRWLPGQRLPHALRITIGSEKHMQDVAGILTSLVRQ 367
            L+LFEG+LTAE AYK LMD GY  RWLPGQ LPH LRITIG+E+  + VA IL  LV +
Sbjct: 309 VLVLFEGALTAEAAYKGLMDEGYIVRWLPGQGLPHGLRITIGTEEETRAVAAILNKLVAE 368


Lambda     K      H
   0.318    0.133    0.400 

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: 458
Number of extensions: 14
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: 369
Length of database: 376
Length adjustment: 30
Effective length of query: 339
Effective length of database: 346
Effective search space:   117294
Effective search space used:   117294
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2299 Ga0059261_2299 (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.17851.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    4.8e-96  307.6   0.0    5.5e-96  307.4   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2299  Ga0059261_2299 histidinol-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2299  Ga0059261_2299 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.4   0.0   5.5e-96   5.5e-96       4     348 ..      14     364 ..      11     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 307.4 bits;  conditional E-value: 5.5e-96
                                 TIGR01141   4 ikklepYqpgarelgek.evvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgve 71 
                                               i +++pY+pg++++ +  + +kL+snEnP+g+s+k+++a+  ++++l+rYpd++a+el+eala+  g++
  lcl|FitnessBrowser__Korea:Ga0059261_2299  14 IMDIAPYVPGKSKTDDGrKAIKLSSNENPLGTSDKARAAFATAANSLERYPDASAVELREALAELHGLD 82 
                                               7899*****9433333358************************************************** PP

                                 TIGR01141  72 eenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140
                                               ++ i+ gnGsde+++l + af+ pgd+++++++ +++Y++ +k  ga  + v++++d   d++a+l+ +
  lcl|FitnessBrowser__Korea:Ga0059261_2299  83 AARIIYGNGSDEVLHLAAGAFAGPGDEIIYVNYGFTVYPIATKRVGATPV-VAADADYATDVDAILASV 150
                                               *******************************************9999876.445555579********* PP

                                 TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFsee...asvlellaeypnlvvl 205
                                               ++++++vf+a+PnnPtG++ +reei ++ +  + d l V+D+AY e+ e       +el++  pn++v+
  lcl|FitnessBrowser__Korea:Ga0059261_2299 151 TDRTRIVFVANPNNPTGTYASREEIARLHAGLRpDILLVLDHAYAEYIEGeidDGGMELAKTQPNVLVT 219
                                               ********************************66**************98777789************* PP

                                 TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererll 274
                                               rT+SK++gLA+ R+G ++++ae+iea++++r p++++    +aa+aal+ds+++e+t  ++++ r++  
  lcl|FitnessBrowser__Korea:Ga0059261_2299 220 RTFSKLYGLAAERIGWGYGSAEVIEAMHRIRLPFSITIAGTAAAIAALHDSAFVEHTRSHNAQWRRWFA 288
                                               ********************************************************************* PP

                                 TIGR01141 275 eelkkle..glevyeSkaNFvlikvke..daeelleallekgiivRdlksaeglleeclRitvGtreen 339
                                               +e++kl   gl+ ++S+aNFvl+ ++   +ae++++ l+++g+ivR l  + gl ++ lRit+Gt+ee+
  lcl|FitnessBrowser__Korea:Ga0059261_2299 289 DEIAKLGnaGLRAVPSQANFVLVLFEGalTAEAAYKGLMDEGYIVRWLPGQ-GL-PHGLRITIGTEEET 355
                                               ****98622688*************9999*******************988.85.************** PP

                                 TIGR01141 340 erllealke 348
                                               +++ ++l++
  lcl|FitnessBrowser__Korea:Ga0059261_2299 356 RAVAAILNK 364
                                               **9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (376 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: 11.45
//
[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