Alignments for a candidate for hisC in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Desulfotalea psychrophila LSv54

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011187887.1 DP_RS03205 histidinol-phosphate aminotransferase

Query= curated2:Q6AQK2
         (379 letters)



>NCBI__GCF_000025945.1:WP_011187887.1
          Length = 379

 Score =  761 bits (1965), Expect = 0.0
 Identities = 379/379 (100%), Positives = 379/379 (100%)

Query: 1   MPLFQKEIALKLDIPENIENIKPYPPGKPLDELEREYGITDSIKLASNENPWGASPKAIK 60
           MPLFQKEIALKLDIPENIENIKPYPPGKPLDELEREYGITDSIKLASNENPWGASPKAIK
Sbjct: 1   MPLFQKEIALKLDIPENIENIKPYPPGKPLDELEREYGITDSIKLASNENPWGASPKAIK 60

Query: 61  AIGESLGDMQRYPDGSAYYLTEAIAKYAGVGMSEIILGNGSNEVIEFLVKAFVQDDSEVI 120
           AIGESLGDMQRYPDGSAYYLTEAIAKYAGVGMSEIILGNGSNEVIEFLVKAFVQDDSEVI
Sbjct: 61  AIGESLGDMQRYPDGSAYYLTEAIAKYAGVGMSEIILGNGSNEVIEFLVKAFVQDDSEVI 120

Query: 121 TSHPSFLMYQKFVQVRGGVNRVIPLKDMHHDLQTILDTVNEKTRLIFIDNPNNPTGTYLE 180
           TSHPSFLMYQKFVQVRGGVNRVIPLKDMHHDLQTILDTVNEKTRLIFIDNPNNPTGTYLE
Sbjct: 121 TSHPSFLMYQKFVQVRGGVNRVIPLKDMHHDLQTILDTVNEKTRLIFIDNPNNPTGTYLE 180

Query: 181 PELLIDFINSLPEHVILVLDEAYVDFMDLDKWLDVPSLIKNQAGRCGIVSLRTFSKAYGL 240
           PELLIDFINSLPEHVILVLDEAYVDFMDLDKWLDVPSLIKNQAGRCGIVSLRTFSKAYGL
Sbjct: 181 PELLIDFINSLPEHVILVLDEAYVDFMDLDKWLDVPSLIKNQAGRCGIVSLRTFSKAYGL 240

Query: 241 SGLRVGFGLMAEEIVTCLHKVRQPFNVNSLAQVGALAALGDVDFYEQTLLKNRQGMKWLM 300
           SGLRVGFGLMAEEIVTCLHKVRQPFNVNSLAQVGALAALGDVDFYEQTLLKNRQGMKWLM
Sbjct: 241 SGLRVGFGLMAEEIVTCLHKVRQPFNVNSLAQVGALAALGDVDFYEQTLLKNRQGMKWLM 300

Query: 301 KEIKGLGCEPFASQTNFFLIDVQGNADKLYTEMLYKGVIIRSMSAYGYPHYIRVTVGTTV 360
           KEIKGLGCEPFASQTNFFLIDVQGNADKLYTEMLYKGVIIRSMSAYGYPHYIRVTVGTTV
Sbjct: 301 KEIKGLGCEPFASQTNFFLIDVQGNADKLYTEMLYKGVIIRSMSAYGYPHYIRVTVGTTV 360

Query: 361 ENKRFLKALSDCLKELNYV 379
           ENKRFLKALSDCLKELNYV
Sbjct: 361 ENKRFLKALSDCLKELNYV 379


Lambda     K      H
   0.320    0.139    0.407 

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: 695
Number of extensions: 7
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: 379
Length of database: 379
Length adjustment: 30
Effective length of query: 349
Effective length of database: 349
Effective search space:   121801
Effective search space used:   121801
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: 50 (23.9 bits)

Align candidate WP_011187887.1 DP_RS03205 (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.1640.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.3e-106  341.0   0.0   3.7e-106  340.9   0.0    1.0  1  lcl|NCBI__GCF_000025945.1:WP_011187887.1  DP_RS03205 histidinol-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_011187887.1  DP_RS03205 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.9   0.0  3.7e-106  3.7e-106       2     347 ..      16     370 ..      15     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 340.9 bits;  conditional E-value: 3.7e-106
                                 TIGR01141   2 ekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkeal 64 
                                               e+i++++pY pg      +re+g+++ +kL+snEnP+g s+k+++a+ e+l +++rYpd +a+ l+ea+
  lcl|NCBI__GCF_000025945.1:WP_011187887.1  16 ENIENIKPYPPGkpldelEREYGITDSIKLASNENPWGASPKAIKAIGESLGDMQRYPDGSAYYLTEAI 84 
                                               689****************************************************************** PP

                                 TIGR01141  65 akylgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedl 133
                                               aky+gv++ +i+lgnGs+e+ie+l++af+++  +v++++p++ mY+  ++++g   + +plk+  ++dl
  lcl|NCBI__GCF_000025945.1:WP_011187887.1  85 AKYAGVGMSEIILGNGSNEVIEFLVKAFVQDDSEVITSHPSFLMYQKFVQVRGGVNRVIPLKDM-HHDL 152
                                               *************************************************************998.8*** PP

                                 TIGR01141 134 eavleaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFsee......asvlel 195
                                               + +l++++ek++l+f+ +PnnPtG++l+ e +++++++  e+++ V+DeAY++F +       +s ++ 
  lcl|NCBI__GCF_000025945.1:WP_011187887.1 153 QTILDTVNEKTRLIFIDNPNNPTGTYLEPELLIDFINSLpEHVILVLDEAYVDFMDLdkwldvPSLIKN 221
                                               ***************************************89**************98788777777777 PP

                                 TIGR01141 196 laeypnlvvlrTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsdkiektve 264
                                                a +  +v lrT+SKa+gL glRvG++++ +ei+  l+kvr+p+nv+sla+  a+aal d d++e+t+ 
  lcl|NCBI__GCF_000025945.1:WP_011187887.1 222 QAGRCGIVSLRTFSKAYGLSGLRVGFGLMAEEIVTCLHKVRQPFNVNSLAQVGALAALGDVDFYEQTLL 290
                                               777789*************************************************************** PP

                                 TIGR01141 265 evkkererlleelkkleglevyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitv 333
                                               ++++++++l++e+k l g e + S++NF li+v+ +a++l+ ++l kg+i+R+++++ g  ++++R+tv
  lcl|NCBI__GCF_000025945.1:WP_011187887.1 291 KNRQGMKWLMKEIKGL-GCEPFASQTNFFLIDVQGNADKLYTEMLYKGVIIRSMSAY-GY-PHYIRVTV 356
                                               ****************.8*************************************99.85.******** PP

                                 TIGR01141 334 Gtreenerllealk 347
                                               Gt  en+r+l+al+
  lcl|NCBI__GCF_000025945.1:WP_011187887.1 357 GTTVENKRFLKALS 370
                                               ************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (379 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: 11.21
//
[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