Alignments for a candidate for hisC in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Thiomicrospira cyclica ALM1

Align histidinol-phosphate aminotransferase [EC:2.6.1.9] (characterized)
to candidate WP_013835367.1 THICY_RS04220 histidinol-phosphate transaminase

Query= reanno::Phaeo:GFF2492
         (361 letters)



>NCBI__GCF_000214825.1:WP_013835367.1
          Length = 363

 Score =  232 bits (591), Expect = 1e-65
 Identities = 134/335 (40%), Positives = 194/335 (57%), Gaps = 4/335 (1%)

Query: 25  GMSNVTKLSSNENPLGPSPKAIEAMQAAVSEMHRYPSSDHSGLRQAIGEVYGLPMEQIIC 84
           G+S VTKL+SNENPLG S K  +A + A+  + RYP  +   LR AI E     M +++ 
Sbjct: 31  GLSRVTKLASNENPLGVSAKVEQAAKLALKTLGRYPDGNAFYLRAAIAEFTCRTMPEVMV 90

Query: 85  GAGSDEIITFLCQAYAGPGDEVLFTEHGFAMYRISALAAGATPVEVAERDRVTDVDALLA 144
           G GS+E++ F+ + +AGPGDEV+F+++ FA+Y I+A   GATP++V  +    D+DA+ A
Sbjct: 91  GNGSNELLEFVGRVFAGPGDEVIFSQYAFAVYAITAQIIGATPIQVTAKAYGHDLDAMAA 150

Query: 145 GCTERTRLVFIANPNNPTGTMIGMADLARLADGLPKGALLVLDGAYAEYVEGYDA--GAA 202
             T +T+L+++ANPNNPTG+      L      +P   ++V D AY EYVE  DA  G A
Sbjct: 151 AITSKTKLIYLANPNNPTGSFFSADALTAFMQKVPANVVVVYDEAYLEYVERDDAPSGLA 210

Query: 203 LVANRDNVVMTRTFSKIYGLGGARVGWGYAPKPIIDVLNRVRGPFNLSSTALAGAEAAVR 262
           L+    NV++TRTFSK YGL   RVG+  A   I+++LNR+R PFN++  +   A AA+ 
Sbjct: 211 LLDQYPNVIVTRTFSKAYGLAALRVGYLLAHPDIVNLLNRIRAPFNVNELSQVCAVAALA 270

Query: 263 DTDYTEHCRKENAKWRTWLAEALAELGVPSDTSCANFILARFASPEEAGACDAFLQSRGL 322
           D D+       N + R+ +  AL  +G     S  NF+      PE A      LQ  G+
Sbjct: 271 DQDFVAASVALNKQERSKVITALTHMGYTPLPSEGNFVCVNM-GPEAASINQQLLQ-LGV 328

Query: 323 IVRRVTGYKLPAALRITVGDETACNALVAAMKVFK 357
           IVR V  Y +   LRI++G E     L+ A+   K
Sbjct: 329 IVRPVANYGMADFLRISIGTEAENQHLITALAQVK 363


Lambda     K      H
   0.318    0.134    0.399 

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: 333
Number of extensions: 15
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: 361
Length of database: 363
Length adjustment: 29
Effective length of query: 332
Effective length of database: 334
Effective search space:   110888
Effective search space used:   110888
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_013835367.1 THICY_RS04220 (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.24522.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-109  351.4   0.1   2.7e-109  351.2   0.1    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013835367.1  THICY_RS04220 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013835367.1  THICY_RS04220 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.2   0.1  2.7e-109  2.7e-109       2     348 ..       9     361 ..       8     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 351.2 bits;  conditional E-value: 2.7e-109
                                 TIGR01141   2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 
                                               ++i k++pY pg      +relg + v kL+snEnP+g+s kv +a+k +lk+l rYpd +a+ l++a+
  lcl|NCBI__GCF_000214825.1:WP_013835367.1   9 PHIAKISPYIPGkpvselQRELGLSRVTKLASNENPLGVSAKVEQAAKLALKTLGRYPDGNAFYLRAAI 77 
                                               5799***************************************************************** PP

                                 TIGR01141  65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133
                                               a+++  ++ ++++gnGs+el+e++ r f+ pgd+v+++++++++Y+++a+i ga  ++v +k+ g +dl
  lcl|NCBI__GCF_000214825.1:WP_013835367.1  78 AEFTCRTMPEVMVGNGSNELLEFVGRVFAGPGDEVIFSQYAFAVYAITAQIIGATPIQVTAKAYG-HDL 145
                                               ***************************************************************96.9** PP

                                 TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee...asvlellae 198
                                               +a+++a+++k+kl++la+PnnPtG++++++ +++++++v ++++VV DeAY e+ e+   +s l ll +
  lcl|NCBI__GCF_000214825.1:WP_013835367.1 146 DAMAAAITSKTKLIYLANPNNPTGSFFSADALTAFMQKVpANVVVVYDEAYLEYVERddaPSGLALLDQ 214
                                               ***************************************88***************99999******** PP

                                 TIGR01141 199 ypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektveevk 267
                                               ypn++v+rT+SKa+gLA+lRvGy++a+++i++ l+++rap+nv++l++ +avaal d+d+++++v+ +k
  lcl|NCBI__GCF_000214825.1:WP_013835367.1 215 YPNVIVTRTFSKAYGLAALRVGYLLAHPDIVNLLNRIRAPFNVNELSQVCAVAALADQDFVAASVALNK 283
                                               ********************************************************************* PP

                                 TIGR01141 268 kererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtr 336
                                               +er  ++++l+++ g    +S++NFv +++  +a+ + ++ll+ g+ivR ++++ g+  ++lRi++Gt+
  lcl|NCBI__GCF_000214825.1:WP_013835367.1 284 QERSKVITALTHM-GYTPLPSEGNFVCVNMGPEAASINQQLLQLGVIVRPVANY-GM-ADFLRISIGTE 349
                                               ***********99.899*************99**********************.86.*********** PP

                                 TIGR01141 337 eenerllealke 348
                                                en++l++al++
  lcl|NCBI__GCF_000214825.1:WP_013835367.1 350 AENQHLITALAQ 361
                                               *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (363 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: 8.44
//
[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