Alignments for a candidate for hisC in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Echinicola vietnamensis KMM 6221, DSM 17526

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate Echvi_2458 Echvi_2458 histidinol-phosphate aminotransferase

Query= reanno::Btheta:349730
         (346 letters)



>FitnessBrowser__Cola:Echvi_2458
          Length = 354

 Score =  357 bits (916), Expect = e-103
 Identities = 178/345 (51%), Positives = 246/345 (71%), Gaps = 5/345 (1%)

Query: 4   LQELTRPNIWKLKPYSSARDEYKGAVASVFLDANENPYNL----PHNRYPDPMQWELKTL 59
           L +L RP+I +LKPYSSARDEY G    VFLDANENP+        NRYPDP Q  LK  
Sbjct: 5   LNKLLRPHIAQLKPYSSARDEYTGK-EGVFLDANENPFGSITAESFNRYPDPYQHALKEK 63

Query: 60  LSKIKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRK 119
           +S IK+V  + IF+GNGSDEAIDL+ RAFC P KDN++ + PTYGMY+V AD+N++  ++
Sbjct: 64  ISAIKQVPVEQIFIGNGSDEAIDLLMRAFCRPGKDNIIILPPTYGMYEVSADINDISIKR 123

Query: 120 VLLDENFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEGLVILDEAY 179
           V L  +FQ   + +L A DE TK+IF+CSPNNP+GN + R +I KI+  F+GLV++DEAY
Sbjct: 124 VNLSADFQLRPDAILEAVDENTKIIFICSPNNPSGNKVRRKDILKIIVGFDGLVVVDEAY 183

Query: 180 NDFSEAPSFLEELDKYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPYNVNQ 239
            DFS+ PSF  EL ++PNL+V QTFSKAWG AA+RLGMAFAS  II IL+KIK PYN++ 
Sbjct: 184 IDFSDEPSFTAELPQHPNLLVMQTFSKAWGLAALRLGMAFASLPIIRILNKIKPPYNISG 243

Query: 240 LTQQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCTVRMYPSDSNFFLAKVTDAVK 299
           LTQ+  +  L    ++++ +K + +ERDYL    +K+    +++P+ +NF L +V  A +
Sbjct: 244 LTQETVLKALQDTSKMKQMVKEMLQERDYLLHALSKMDGIKKIHPTHANFVLVEVPAAKE 303

Query: 300 IYNYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAALKKY 344
            Y++L+ + IIVR+R  + LC  CLR++VGTR EN+ L+  L ++
Sbjct: 304 TYDHLIEQQIIVRDRSKVVLCDQCLRISVGTREENDQLIGKLSEF 348


Lambda     K      H
   0.320    0.136    0.402 

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: 369
Number of extensions: 13
Number of successful extensions: 3
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: 346
Length of database: 354
Length adjustment: 29
Effective length of query: 317
Effective length of database: 325
Effective search space:   103025
Effective search space used:   103025
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate Echvi_2458 Echvi_2458 (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.6882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   8.1e-116  372.6   0.0   9.3e-116  372.4   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2458  Echvi_2458 histidinol-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2458  Echvi_2458 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.4   0.0  9.3e-116  9.3e-116       1     348 [.      10     347 ..      10     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.4 bits;  conditional E-value: 9.3e-116
                            TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgveeen 74 
                                          r++i +l+pY+++ +e+++ke v L++nEnPfg         ++e  +++rYpdp + +lke++++  +v +e+
  lcl|FitnessBrowser__Cola:Echvi_2458  10 RPHIAQLKPYSSARDEYTGKEGVFLDANENPFGSI-------TAE--SFNRYPDPYQHALKEKISAIKQVPVEQ 74 
                                          789*********9999*****************88.......344..89************************* PP

                            TIGR01141  75 illgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaakekvklv 147
                                          i++gnGsde+i+ll+raf+ pg d++++l+pty mYevsa+i+++++k v+l +d+q   +a+lea++e++k++
  lcl|FitnessBrowser__Cola:Echvi_2458  75 IFIGNGSDEAIDLLMRAFCRPGkDNIIILPPTYGMYEVSADINDISIKRVNLSADFQLRPDAILEAVDENTKII 148
                                          ************************************************************************** PP

                            TIGR01141 148 flasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrTlSKafgLAglRvGy 221
                                          f++sPnnP+Gn + r++i k++    d+lVVvDeAYi+Fs+e+s++  l ++pnl+v++T+SKa gLA+lR+G+
  lcl|FitnessBrowser__Cola:Echvi_2458 149 FICSPNNPSGNKVRRKDILKIIVGF-DGLVVVDEAYIDFSDEPSFTAELPQHPNLLVMQTFSKAWGLAALRLGM 221
                                          ************************8.9*********************************************** PP

                            TIGR01141 222 aianaeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegle.vyeSkaNFvl 294
                                          a+a+  ii++l+k+++pyn+s l++e+ ++al+d +k+++ v+e+ +er++ll++l+k++g++ + + +aNFvl
  lcl|FitnessBrowser__Cola:Echvi_2458 222 AFASLPIIRILNKIKPPYNISGLTQETVLKALQDTSKMKQMVKEMLQERDYLLHALSKMDGIKkIHPTHANFVL 295
                                          ***************************************************************9999******* PP

                            TIGR01141 295 ikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealke 348
                                          ++v+ +a+e +++l+e++iivRd +++  l+++clRi+vGtreen++l+  l+e
  lcl|FitnessBrowser__Cola:Echvi_2458 296 VEVP-AAKETYDHLIEQQIIVRDRSKV-VLCDQCLRISVGTREENDQLIGKLSE 347
                                          ****.********************99.69*******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (354 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: 12.06
//
[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