Alignments for a candidate for hisC in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Thermocrinis albus DSM 14484

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_012991370.1 THAL_RS01625 histidinol-phosphate transaminase

Query= curated2:O67857
         (354 letters)



>NCBI__GCF_000025605.1:WP_012991370.1
          Length = 351

 Score =  406 bits (1043), Expect = e-118
 Identities = 199/350 (56%), Positives = 263/350 (75%)

Query: 1   MIPQRIKELEAYKTEVTPASVRLSSNEFPYDFPEEIKQRALEELKKVPLNKYPDPEAKEL 60
           MI  RIK L  YKTE   A V+LSSNE   D P E+K+     + ++P N+YPDP+A EL
Sbjct: 1   MISARIKGLSPYKTEKRSAKVKLSSNELSLDLPAEVKEEIARAVARIPFNRYPDPQATEL 60

Query: 61  KAVLADFFGVKEENLVLGNGSDELIYYLSIAIGELYIPVYIPVPTFPMYEISAKVLGRPL 120
           K  +A  FGV    +VLGNGSDELI YL +A+GE    V+ PVPTFPMY ISA+ +G+  
Sbjct: 61  KEAVALRFGVDPSCVVLGNGSDELIQYLCMAVGESGDAVFYPVPTFPMYGISAQTVGKER 120

Query: 121 VKVQLDENFDIDLERSIELIEKEKPVLGYFAYPNNPTGNLFSRGKIEEIRNRGVFCVIDE 180
           ++V L E+ DIDL+ S++ I + KP+L +F+YPNNPTGN F + KI  IRN GVFCVIDE
Sbjct: 121 LEVPLGEDLDIDLDSSLKEIRRRKPILAFFSYPNNPTGNCFDKNKITAIRNEGVFCVIDE 180

Query: 181 AYYHYSGETFLEDALKREDTVVLRTLSKIGMASLRVGILIGKGEIVSEINKVRLPFNVTY 240
           AYYH+SG+TFLE+AL REDTVVLRTLSKIGMA LRVG+LI + ++   IN++RLPFN+TY
Sbjct: 181 AYYHFSGKTFLEEALSREDTVVLRTLSKIGMAGLRVGVLIARQDVADYINRMRLPFNITY 240

Query: 241 PSQVMAKVLLTEGREFLMEKIQEVVKERERMYDEMKKIEGVEVFPSKANFLLFRTPYPAH 300
           PSQV+A ++LT+   F+ E +  V +ER+R+ D ++ ++GVEVFPS+ANF LFRTP PA 
Sbjct: 241 PSQVIAVLMLTKFYHFVEEAVNTVKRERDRLMDALRSMKGVEVFPSEANFFLFRTPLPAP 300

Query: 301 EVYQELLKRDVLVRNVSYMEGLQKCLRVSVGKPEENNKFLEALEESIKSL 350
            + ++LL+  VLVR+VSY+  L++CLRVS+GKPEEN+ FLEAL + I+ +
Sbjct: 301 LLQEKLLEEGVLVRDVSYLPRLERCLRVSIGKPEENDAFLEALHKVIEKM 350


Lambda     K      H
   0.317    0.138    0.383 

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: 416
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: 354
Length of database: 351
Length adjustment: 29
Effective length of query: 325
Effective length of database: 322
Effective search space:   104650
Effective search space used:   104650
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_012991370.1 THAL_RS01625 (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.5394.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-106  341.8   0.0   2.1e-106  341.7   0.0    1.0  1  lcl|NCBI__GCF_000025605.1:WP_012991370.1  THAL_RS01625 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025605.1:WP_012991370.1  THAL_RS01625 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.7   0.0  2.1e-106  2.1e-106       3     348 ..       5     345 ..       3     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 341.7 bits;  conditional E-value: 2.1e-106
                                 TIGR01141   3 kikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelk..klhrYpdpqalelkealakylg 69 
                                               +ik l+pY++ +    +++ vkL+snE  ++ + +vke++ ++++  +++rYpdpqa+elkea+a ++g
  lcl|NCBI__GCF_000025605.1:WP_012991370.1   5 RIKGLSPYKT-E---KRSAKVKLSSNELSLDLPAEVKEEIARAVAriPFNRYPDPQATELKEAVALRFG 69 
                                               7999******.3...334679***********************99999******************** PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplked.gqedleavl 137
                                               v++  ++lgnGsdeli++l++a+ e+gdav ++ pt+ mY +sa++ g e  evpl ed   +   +++
  lcl|NCBI__GCF_000025605.1:WP_012991370.1  70 VDPSCVVLGNGSDELIQYLCMAVGESGDAVFYPVPTFPMYGISAQTVGKERLEVPLGEDlDIDLDSSLK 138
                                               ***********************************************************7777777888 PP

                                 TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleevedalVVvDeAYieFseeasvlellaeypnlvvlr 206
                                               e++ +k+ l f+ +PnnPtGn++++++i+++ +e   +++V+DeAY++Fs++ ++le +  +++ vvlr
  lcl|NCBI__GCF_000025605.1:WP_012991370.1 139 EIRRRKPILAFFSYPNNPTGNCFDKNKITAIRNE--GVFCVIDEAYYHFSGK-TFLEEALSREDTVVLR 204
                                               8********************************9..5**************7.**************** PP

                                 TIGR01141 207 TlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsd.kiektveevkkererll 274
                                               TlSK+  +AglRvG++ia ++++++++++r p+n++++++ +av  l++   ++e+ v+ vk+er+rl+
  lcl|NCBI__GCF_000025605.1:WP_012991370.1 205 TLSKIG-MAGLRVGVLIARQDVADYINRMRLPFNITYPSQVIAVLMLTKFYhFVEEAVNTVKRERDRLM 272
                                               ****97.*****************************************98889**************** PP

                                 TIGR01141 275 eelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerll 343
                                               ++l+ ++g+ev++S+aNF l++++ +a  l e+lle+g++vRd++  +  le clR+++G++een+++l
  lcl|NCBI__GCF_000025605.1:WP_012991370.1 273 DALRSMKGVEVFPSEANFFLFRTPLPAPLLQEKLLEEGVLVRDVSYLP-RLERCLRVSIGKPEENDAFL 340
                                               ********************************************9886.57****************** PP

                                 TIGR01141 344 ealke 348
                                               eal++
  lcl|NCBI__GCF_000025605.1:WP_012991370.1 341 EALHK 345
                                               **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (351 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: 11.45
//
[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