Alignments for a candidate for hisC in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Klebsiella variicola At-22

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate WP_012967604.1 KVAR_RS07950 histidinol-phosphate aminotransferase

Query= SwissProt::P06986
         (356 letters)



>NCBI__GCF_000025465.1:WP_012967604.1
          Length = 353

 Score =  595 bits (1535), Expect = e-175
 Identities = 295/353 (83%), Positives = 321/353 (90%)

Query: 4   VTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQPKAV 63
           ++I DLAR NVR LTPYQSARRLGG GDVWLNANE+PTAV FQLT QT+NRYPE QPKAV
Sbjct: 1   MSIEDLARANVRALTPYQSARRLGGKGDVWLNANEFPTAVAFQLTAQTMNRYPEPQPKAV 60

Query: 64  IENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVE 123
           IE+YA+YA VKPEQVLVSRGADEGIELLIRAFCEPGKDA+LYCPPTYGMYSVSAETIGVE
Sbjct: 61  IESYARYADVKPEQVLVSRGADEGIELLIRAFCEPGKDALLYCPPTYGMYSVSAETIGVE 120

Query: 124 CRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVVA 183
           CRTVPTL +WQLDL GI  +LDGVKVV+VCSPNNPTGQ+I+PQ  R LLE+TR KAIVVA
Sbjct: 121 CRTVPTLADWQLDLPGIEAQLDGVKVVFVCSPNNPTGQIIDPQSIRDLLEMTRDKAIVVA 180

Query: 184 DEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPY 243
           DEAYIEFCPQA+LAGWL++YPHL +LRTLSKAFALAGLRCGFTLAN EVIN+L+KVIAPY
Sbjct: 181 DEAYIEFCPQATLAGWLSDYPHLVVLRTLSKAFALAGLRCGFTLANAEVINVLLKVIAPY 240

Query: 244 PLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYILAR 303
           PLSTPVADIAAQALS +GI AMR+RVAQI+ ER YL+  L+ I CVEQVFDSE NY+LAR
Sbjct: 241 PLSTPVADIAAQALSAEGIAAMRQRVAQILDERRYLVEQLRGIACVEQVFDSEANYVLAR 300

Query: 304 FKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV 356
             ASSAVFKSLWDQGIILRDQNKQPSLSGCLRIT+GTR ESQRVIDAL AE V
Sbjct: 301 ITASSAVFKSLWDQGIILRDQNKQPSLSGCLRITIGTRAESQRVIDALTAENV 353


Lambda     K      H
   0.319    0.135    0.396 

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: 497
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: 356
Length of database: 353
Length adjustment: 29
Effective length of query: 327
Effective length of database: 324
Effective search space:   105948
Effective search space used:   105948
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_012967604.1 KVAR_RS07950 (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.23106.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-126  408.0   0.0   1.6e-126  407.8   0.0    1.0  1  lcl|NCBI__GCF_000025465.1:WP_012967604.1  KVAR_RS07950 histidinol-phosphat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012967604.1  KVAR_RS07950 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.8   0.0  1.6e-126  1.6e-126       1     347 [.       8     349 ..       8     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.8 bits;  conditional E-value: 1.6e-126
                                 TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylg 69 
                                               r+++++l+pYq+ ar+lg+k++v+Ln+nE P+++      +l+++  +++rYp+pq++++ e++a+y++
  lcl|NCBI__GCF_000025465.1:WP_012967604.1   8 RANVRALTPYQS-ARRLGGKGDVWLNANEFPTAVA----FQLTAQ--TMNRYPEPQPKAVIESYARYAD 69 
                                               689*********.9*****************9998....788777..9********************* PP

                                 TIGR01141  70 veeenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavl 137
                                               v++e++l+++G+de+ielliraf+epg da l+++pty mY+vsa++ g+e+++vp+ +d+q dl+ ++
  lcl|NCBI__GCF_000025465.1:WP_012967604.1  70 VKPEQVLVSRGADEGIELLIRAFCEPGkDALLYCPPTYGMYSVSAETIGVECRTVPTLADWQLDLPGIE 138
                                               ***************************9***************************************** PP

                                 TIGR01141 138 eaakekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFseeasvlellaeypnlvvl 205
                                                a+ + vk+vf++sPnnPtG++++ + i+++le++  +a+VV DeAYieF+++a+ + +l++yp+lvvl
  lcl|NCBI__GCF_000025465.1:WP_012967604.1 139 -AQLDGVKVVFVCSPNNPTGQIIDPQSIRDLLEMTrDKAIVVADEAYIEFCPQATLAGWLSDYPHLVVL 206
                                               .**********************************55******************************** PP

                                 TIGR01141 206 rTlSKafgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kiektveevkkerer 272
                                               rTlSKaf+LAglR+G+++anae+i++l kv+apy++s++++++a +al+ +    ++++v+++  er++
  lcl|NCBI__GCF_000025465.1:WP_012967604.1 207 RTLSKAFALAGLRCGFTLANAEVINVLLKVIAPYPLSTPVADIAAQALSAEGiaAMRQRVAQILDERRY 275
                                               ***************************************************9999************** PP

                                 TIGR01141 273 lleelkklegle.vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreene 340
                                               l e+l+ + ++e v++S+aN+vl+++  ++++++++l+++gii+Rd++++++ l++clRit+Gtr e++
  lcl|NCBI__GCF_000025465.1:WP_012967604.1 276 LVEQLRGIACVEqVFDSEANYVLARIT-ASSAVFKSLWDQGIILRDQNKQPS-LSGCLRITIGTRAESQ 342
                                               **************************9.********************9977.6*************** PP

                                 TIGR01141 341 rllealk 347
                                               r+++al 
  lcl|NCBI__GCF_000025465.1:WP_012967604.1 343 RVIDALT 349
                                               ****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (353 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: 7.53
//
[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