Alignments for a candidate for hisC in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Klebsiella michiganensis M5al

Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate BWI76_RS18930 BWI76_RS18930 histidinol-phosphate transaminase

Query= SwissProt::P06986
         (356 letters)



>FitnessBrowser__Koxy:BWI76_RS18930
          Length = 353

 Score =  611 bits (1575), Expect = e-179
 Identities = 303/353 (85%), Positives = 328/353 (92%)

Query: 4   VTITDLARENVRNLTPYQSARRLGGNGDVWLNANEYPTAVEFQLTQQTLNRYPECQPKAV 63
           ++I DLAR NVR LTPYQSARRLGG GDVWLNANE+PTAVEFQLT+QT+NRYPE QPKAV
Sbjct: 1   MSIEDLARANVRALTPYQSARRLGGKGDVWLNANEFPTAVEFQLTEQTMNRYPEPQPKAV 60

Query: 64  IENYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVE 123
           IE YAQYAGVKPEQVLVSRGADEGIELLIRAFCEPG+DA+LYCPPTYGMYSVSAETIGV 
Sbjct: 61  IERYAQYAGVKPEQVLVSRGADEGIELLIRAFCEPGQDAVLYCPPTYGMYSVSAETIGVT 120

Query: 124 CRTVPTLDNWQLDLQGISDKLDGVKVVYVCSPNNPTGQLINPQDFRTLLELTRGKAIVVA 183
           CRTVPTL +WQLDL GI+  LDGVKVV+VCSPNNPTGQ+INP+DFRTLLE+TRGKAIVVA
Sbjct: 121 CRTVPTLADWQLDLPGIAANLDGVKVVFVCSPNNPTGQIINPKDFRTLLEMTRGKAIVVA 180

Query: 184 DEAYIEFCPQASLAGWLAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPY 243
           DEAYIEFCPQA+LA WL EYPHLAILRTLSKAFALAGLRCGFTLAN EVIN+LMKVIAPY
Sbjct: 181 DEAYIEFCPQATLATWLNEYPHLAILRTLSKAFALAGLRCGFTLANAEVINVLMKVIAPY 240

Query: 244 PLSTPVADIAAQALSPQGIVAMRERVAQIIAEREYLIAALKEIPCVEQVFDSETNYILAR 303
           PLSTPVADIAAQALS +GI AMR RVAQI+AER+YL++ L+ I CVE+VFDSE+NY+LAR
Sbjct: 241 PLSTPVADIAAQALSAEGIAAMRARVAQILAERDYLVSQLRGIACVEEVFDSESNYVLAR 300

Query: 304 FKASSAVFKSLWDQGIILRDQNKQPSLSGCLRITVGTREESQRVIDALRAEQV 356
             ASSAVFKSLWDQGIILRDQNKQPSLSGCLRIT+GTR ESQRVIDAL AE V
Sbjct: 301 IVASSAVFKSLWDQGIILRDQNKQPSLSGCLRITIGTRAESQRVIDALTAENV 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: 510
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 BWI76_RS18930 BWI76_RS18930 (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.31637.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.6e-126  405.8   0.0   7.5e-126  405.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS18930  BWI76_RS18930 histidinol-phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS18930  BWI76_RS18930 histidinol-phosphate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.6   0.0  7.5e-126  7.5e-126       1     347 [.       8     349 ..       8     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 405.6 bits;  conditional E-value: 7.5e-126
                               TIGR01141   1 rekikklepYqpgarelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealakylgve 71 
                                             r+++++l+pYq+ ar+lg+k++v+Ln+nE P++++     +l+e+  +++rYp+pq++++ e++a+y+gv+
  lcl|FitnessBrowser__Koxy:BWI76_RS18930   8 RANVRALTPYQS-ARRLGGKGDVWLNANEFPTAVE----FQLTEQ--TMNRYPEPQPKAVIERYAQYAGVK 71 
                                             689*********.9*******************99....899888..9*********************** PP

                               TIGR01141  72 eenillgnGsdelielliraflepg.davlvleptysmYevsakiagaevkevplkedgqedleavleaak 141
                                             +e++l+++G+de+ielliraf+epg davl+++pty mY+vsa++ g+ +++vp+ +d+q dl+ ++ a+ 
  lcl|FitnessBrowser__Koxy:BWI76_RS18930  72 PEQVLVSRGADEGIELLIRAFCEPGqDAVLYCPPTYGMYSVSAETIGVTCRTVPTLADWQLDLPGIA-ANL 141
                                             *******************************************************************.*** PP

                               TIGR01141 142 ekvklvflasPnnPtGnllkreeiekvleeve.dalVVvDeAYieFseeasvlellaeypnlvvlrTlSKa 211
                                             + vk+vf++sPnnPtG++++ ++++++le+++ +a+VV DeAYieF+++a+ + +l+eyp+l++lrTlSKa
  lcl|FitnessBrowser__Koxy:BWI76_RS18930 142 DGVKVVFVCSPNNPTGQIINPKDFRTLLEMTRgKAIVVADEAYIEFCPQATLATWLNEYPHLAILRTLSKA 212
                                             *******************************55************************************** PP

                               TIGR01141 212 fgLAglRvGyaianaeiiealekvrapynvsslaleaavaalrdsd..kiektveevkkererlleelkkl 280
                                             f+LAglR+G+++anae+i++l+kv+apy++s++++++a +al+ +    ++++v+++ +er++l ++l+ +
  lcl|FitnessBrowser__Koxy:BWI76_RS18930 213 FALAGLRCGFTLANAEVINVLMKVIAPYPLSTPVADIAAQALSAEGiaAMRARVAQILAERDYLVSQLRGI 283
                                             *********************************************9999********************** PP

                               TIGR01141 281 egle.vyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerllealk 347
                                              ++e v++S+ N+vl+++  ++++++++l+++gii+Rd++++++ l++clRit+Gtr e++r+++al 
  lcl|FitnessBrowser__Koxy:BWI76_RS18930 284 ACVEeVFDSESNYVLARIV-ASSAVFKSLWDQGIILRDQNKQPS-LSGCLRITIGTRAESQRVIDALT 349
                                             ******************9.********************9977.6*******************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 6.80
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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