Alignments for a candidate for hisC in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Alicycliphilus denitrificans K601

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_013518089.1 ALIDE2_RS18250 histidinol-phosphate transaminase

Query= reanno::psRCH2:GFF3234
         (348 letters)



>NCBI__GCF_000204645.1:WP_013518089.1
          Length = 360

 Score =  410 bits (1054), Expect = e-119
 Identities = 217/349 (62%), Positives = 259/349 (74%), Gaps = 7/349 (2%)

Query: 6   SPFVKDLVPYVPGEQPKLSKLVKLNTNENPYGPSPRAIAAMQAELNDSLRLYPDPNGERL 65
           SP V  L PYVPGEQP+++ LVKLNTNENPY PSPRA+AA++A   + L+LYPDP    L
Sbjct: 8   SPVVGRLEPYVPGEQPRIAGLVKLNTNENPYPPSPRAVAAIEAAAREGLQLYPDPQSLAL 67

Query: 66  KQAVADYYGVQPAQVFVGNGSDEVLAHAFHGLFQHAG-PLLFPDISYSFYPVYCGLYGIA 124
           ++ +A ++G++  QVFVGNGSDEVLAHAF   FQHAG PLL PDI+YSFY VYC L+GIA
Sbjct: 68  RETIAAHHGLEAGQVFVGNGSDEVLAHAFFAFFQHAGQPLLMPDITYSFYRVYCRLWGIA 127

Query: 125 YETVALDEQFQIDVADY-----NRPNGGIIFPNPNAPTGCLLALEAIERLLQANTETVVL 179
            E   LDE   IDV             GI+  NPNAPTG  L L  IERLL A  + VVL
Sbjct: 128 PELQPLDEGLAIDVERIAARAAEGACAGIVLANPNAPTGMGLPLSQIERLLAACPQRVVL 187

Query: 180 VDEAYVDFGGESAIALVDRYPNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSF 239
           VDEAYVDFGGESA++LV RYPNLLV  TLSKSRSLAGLRVG A G   LI+ALER+K+SF
Sbjct: 188 VDEAYVDFGGESAVSLVPRYPNLLVVHTLSKSRSLAGLRVGAAFGQRPLIDALERVKDSF 247

Query: 240 NSYPLDRIAIAGAAAAFEDRAYFQQTCQQVIDSREAVVAAMQGLGFEVLPSAANFIFARH 299
           NSYPLDR+A AGA AA+ED AYF +T + V+ SRE +  A++ LGFEVLPS ANF+F RH
Sbjct: 248 NSYPLDRLAQAGARAAYEDVAYFDETRRAVMHSREGLALALEDLGFEVLPSQANFLFVRH 307

Query: 300 PQRDAATIAASLREQGVIVRHF-KQRRIEQFLRITIGTPEQNQALLEAL 347
           P  D A +AA+LRE+ V+VRHF +  RI Q+LRI++GTP Q  AL+ AL
Sbjct: 308 PAHDGARLAAALRERAVLVRHFARPERIAQYLRISVGTPAQCDALVRAL 356


Lambda     K      H
   0.320    0.137    0.401 

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: 456
Number of extensions: 19
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: 348
Length of database: 360
Length adjustment: 29
Effective length of query: 319
Effective length of database: 331
Effective search space:   105589
Effective search space used:   105589
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 WP_013518089.1 ALIDE2_RS18250 (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.5258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      5e-88  281.2   0.0    5.6e-88  281.1   0.0    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013518089.1  ALIDE2_RS18250 histidinol-phosph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013518089.1  ALIDE2_RS18250 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.1   0.0   5.6e-88   5.6e-88       4     348 ..      11     358 ..       8     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 281.1 bits;  conditional E-value: 5.6e-88
                                 TIGR01141   4 ikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk.klhrYpdpqalelkealakylgve 71 
                                               +  lepY+pg++   + + vkLn+nEnP++ps+++++a++++++  l++Ypdpq+l+l+e++a++ g+e
  lcl|NCBI__GCF_000204645.1:WP_013518089.1  11 VGRLEPYVPGEQPR-IAGLVKLNTNENPYPPSPRAVAAIEAAAReGLQLYPDPQSLALRETIAAHHGLE 78 
                                               6789*****95554.448***********************99889*********************** PP

                                 TIGR01141  72 eenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavle. 138
                                               + ++++gnGsde++   + af +   +  l+++ tys Y+v+ ++ g+     pl+e    d+e +++ 
  lcl|NCBI__GCF_000204645.1:WP_013518089.1  79 AGQVFVGNGSDEVLAHAFFAFFQHAgQPLLMPDITYSFYRVYCRLWGIAPELQPLDEGLAIDVERIAAr 147
                                               ***************99999988777********************************98999999986 PP

                                 TIGR01141 139 aakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlrT 207
                                               aa+     + la+Pn+PtG  l  ++ie++l++  + +V+vDeAY++F +e s+++l+ +ypnl+v+ T
  lcl|NCBI__GCF_000204645.1:WP_013518089.1 148 AAEGACAGIVLANPNAPTGMGLPLSQIERLLAACPQRVVLVDEAYVDFGGE-SAVSLVPRYPNLLVVHT 215
                                               7777788899***********************989**************7.***************** PP

                                 TIGR01141 208 lSKafgLAglRvGyaianaeiiealekvrapyn...vsslaleaavaalrdsdkiektveevkkererl 273
                                               lSK+ +LAglRvG a+++  +i+ale+v++++n   +++la++ a aa++d +++ +t ++v ++re l
  lcl|NCBI__GCF_000204645.1:WP_013518089.1 216 LSKSRSLAGLRVGAAFGQRPLIDALERVKDSFNsypLDRLAQAGARAAYEDVAYFDETRRAVMHSREGL 284
                                               *****************************87543339******************************** PP

                                 TIGR01141 274 leelkkleglevyeSkaNFvlikvke.daeelleallekgiivRdlksaeglleeclRitvGtreener 341
                                                 +l++l g+ev +S+aNF++++ ++ d ++l+ al e+ ++vR+++  e  + ++lRi+vGt+ ++++
  lcl|NCBI__GCF_000204645.1:WP_013518089.1 285 ALALEDL-GFEVLPSQANFLFVRHPAhDGARLAAALRERAVLVRHFARPE-RIAQYLRISVGTPAQCDA 351
                                               *******.8***************99999*****************9875.68**************** PP

                                 TIGR01141 342 llealke 348
                                               l++al+ 
  lcl|NCBI__GCF_000204645.1:WP_013518089.1 352 LVRALQA 358
                                               ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (360 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: 9.35
//
[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