Alignments for a candidate for hisC in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Frankia alni ACN14A

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011606115.1 FRAAL_RS21810 histidinol-phosphate transaminase

Query= curated2:Q2J8K9
         (397 letters)



>NCBI__GCF_000058485.1:WP_011606115.1
          Length = 402

 Score =  671 bits (1732), Expect = 0.0
 Identities = 337/390 (86%), Positives = 354/390 (90%)

Query: 6   AGSGAEDRPWRPWDADGLPLRDSLRGLSPYGAPQLDVPVRLNTNENPHPPSVGLVDAIGK 65
           AG   +DRPWRP D DGLPLRDSLRGLSPYGAPQLDVPV LNTNENPHPPS+GLVDA+GK
Sbjct: 11  AGPAGDDRPWRPLDIDGLPLRDSLRGLSPYGAPQLDVPVLLNTNENPHPPSIGLVDALGK 70

Query: 66  AAALAATEANRYPDRDAEALRADLAYYLTPDAGFGVHTSQVWAANGSNEILQQLLQAFGG 125
           AA L ATEANRYPDRDAEALRADLAYYLTPDAGFGVHT+QVWAANGSNEILQQL QAFGG
Sbjct: 71  AATLVATEANRYPDRDAEALRADLAYYLTPDAGFGVHTAQVWAANGSNEILQQLCQAFGG 130

Query: 126 PGRVALGFEPSYSMHRLIALATATEWVAGQRAEDFTLSPAVVTDAIARHRPALVFLCSPN 185
           PGRVA+GFEPSYSMHRLIALATATEWV  +RA DFTLS   VT A+ RHRPAL+FLCSPN
Sbjct: 131 PGRVAVGFEPSYSMHRLIALATATEWVREERAADFTLSAETVTAAVERHRPALLFLCSPN 190

Query: 186 NPTGTALPPEVVAAACEAVEATGSGMVVVDEAYAEFRRAGVPSTLTLLPRHPRLVVTRTM 245
           NPTGTALP +VV AACEA+   GSGMVVVDEAYAEFRRAGVPS LTLLPRHPRL+VTRTM
Sbjct: 191 NPTGTALPLDVVVAACEAMARVGSGMVVVDEAYAEFRRAGVPSALTLLPRHPRLIVTRTM 250

Query: 246 SKAFALAGARVGYLAAHPAVVDSLYLVRLPYHLSSFTQAVARTALAHADELLGTVEAVKA 305
           SKAFALAGARVGYLAAHPAVVD+L LVRLPYHLSSFTQAVARTALAHADELL TVEAVKA
Sbjct: 251 SKAFALAGARVGYLAAHPAVVDALQLVRLPYHLSSFTQAVARTALAHADELLATVEAVKA 310

Query: 306 QRDRIVRELPALGLRLAPSDANFVFFGRFADQRAVWQSLLDAGVLVRDVGLTGWLRVTAG 365
           QRDRIV EL ALGLRLAPSDANFVFFG FADQRAVW+ LLDAGVLVRDVGL GWLRVTAG
Sbjct: 311 QRDRIVVELGALGLRLAPSDANFVFFGLFADQRAVWRGLLDAGVLVRDVGLPGWLRVTAG 370

Query: 366 LPNEVDAFLGALGRTLTGSVIGADGVISLA 395
           LP EVDAFL ALGR L GS + ADG+++LA
Sbjct: 371 LPAEVDAFLAALGRVLAGSDVAADGIVTLA 400


Lambda     K      H
   0.320    0.135    0.403 

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: 638
Number of extensions: 17
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: 397
Length of database: 402
Length adjustment: 31
Effective length of query: 366
Effective length of database: 371
Effective search space:   135786
Effective search space used:   135786
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: 50 (23.9 bits)

Align candidate WP_011606115.1 FRAAL_RS21810 (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.7630.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.4e-95  305.3   0.0    2.7e-95  305.1   0.0    1.0  1  lcl|NCBI__GCF_000058485.1:WP_011606115.1  FRAAL_RS21810 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011606115.1  FRAAL_RS21810 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.1   0.0   2.7e-95   2.7e-95       1     348 [.      31     384 ..      31     385 .. 0.96

  Alignments for each domain:
  == domain 1  score: 305.1 bits;  conditional E-value: 2.7e-95
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk....klhrYpdpqalelkeala 65 
                                               r++++ l+pY ++      +  v Ln+nEnP++ps  +++al ++++    + +rYpd++a +l+++la
  lcl|NCBI__GCF_000058485.1:WP_011606115.1  31 RDSLRGLSPYGAP----QLDVPVLLNTNENPHPPSIGLVDALGKAATlvatEANRYPDRDAEALRADLA 95 
                                               67899999**995....55679********************999888889****************** PP

                                 TIGR01141  66 kylg......veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked 128
                                                yl+      v++++++++nGs+e+++ l++af  pg+ ++ +ep+ysm++++a ++ +e++  + ++d
  lcl|NCBI__GCF_000058485.1:WP_011606115.1  96 YYLTpdagfgVHTAQVWAANGSNEILQQLCQAFGGPGRVAVGFEPSYSMHRLIALATATEWVREERAAD 164
                                               ***99**************************************************************** PP

                                 TIGR01141 129 gqedleavle.aakekvklvflasPnnPtGnllkreeiekvleev.e..dalVVvDeAYieFsee..as 191
                                               ++   e v + ++ +++ l fl+sPnnPtG+ l  + +++ +e++ +  +++VVvDeAY eF +   +s
  lcl|NCBI__GCF_000058485.1:WP_011606115.1 165 FTLSAETVTAaVERHRPALLFLCSPNNPTGTALPLDVVVAACEAMaRvgSGMVVVDEAYAEFRRAgvPS 233
                                               877777777658999************************99999864579************99988** PP

                                 TIGR01141 192 vlellaeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkie 260
                                               +l ll ++p l+v+rT+SKaf+LAg RvGy+ a++++++al+ vr py++ss ++++a +al ++d++ 
  lcl|NCBI__GCF_000058485.1:WP_011606115.1 234 ALTLLPRHPRLIVTRTMSKAFALAGARVGYLAAHPAVVDALQLVRLPYHLSSFTQAVARTALAHADELL 302
                                               ********************************************************************* PP

                                 TIGR01141 261 ktveevkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleecl 329
                                               +tve+vk++r+r+  el +l gl+  +S+aNFv++ + +d++++++ ll++g++vRd++     l+++l
  lcl|NCBI__GCF_000058485.1:WP_011606115.1 303 ATVEAVKAQRDRIVVELGAL-GLRLAPSDANFVFFGLFADQRAVWRGLLDAGVLVRDVG-----LPGWL 365
                                               ********************.8************************************7.....599** PP

                                 TIGR01141 330 RitvGtreenerllealke 348
                                               R+t G + e +++l+al +
  lcl|NCBI__GCF_000058485.1:WP_011606115.1 366 RVTAGLPAEVDAFLAALGR 384
                                               ****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (402 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: 10.67
//
[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