Alignments for a candidate for hisC in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisC in Caulobacter crescentus NA1000

Align Histidinol-phosphate aminotransferase 2; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 2 (uncharacterized)
to candidate CCNA_02617 CCNA_02617 histidinol-phosphate aminotransferase

Query= curated2:Q9A5B6
         (378 letters)



>FitnessBrowser__Caulo:CCNA_02617
          Length = 378

 Score =  749 bits (1935), Expect = 0.0
 Identities = 378/378 (100%), Positives = 378/378 (100%)

Query: 1   MERGRMLVLDRKPLTPAWASPMRQALEGVQGYKAGMTLAEAARRTGLSAFSKLASNENLL 60
           MERGRMLVLDRKPLTPAWASPMRQALEGVQGYKAGMTLAEAARRTGLSAFSKLASNENLL
Sbjct: 1   MERGRMLVLDRKPLTPAWASPMRQALEGVQGYKAGMTLAEAARRTGLSAFSKLASNENLL 60

Query: 61  GPSPKVAEAVMAAMAEPHIYPDPHSDVLRAAIGARLGVSPARVVVSPGSEALIDYVFRAV 120
           GPSPKVAEAVMAAMAEPHIYPDPHSDVLRAAIGARLGVSPARVVVSPGSEALIDYVFRAV
Sbjct: 61  GPSPKVAEAVMAAMAEPHIYPDPHSDVLRAAIGARLGVSPARVVVSPGSEALIDYVFRAV 120

Query: 121 LHPGDSILLSSPTFPTYEIFGRCAEARIIDVPRLANFDIDVPAVCAAAALGPKLLVLCTP 180
           LHPGDSILLSSPTFPTYEIFGRCAEARIIDVPRLANFDIDVPAVCAAAALGPKLLVLCTP
Sbjct: 121 LHPGDSILLSSPTFPTYEIFGRCAEARIIDVPRLANFDIDVPAVCAAAALGPKLLVLCTP 180

Query: 181 NNPTGNALKAADFQAILAATPRSTVVFVDEAYREYHEAFDTFAMLDAWGGPWVSARTFSK 240
           NNPTGNALKAADFQAILAATPRSTVVFVDEAYREYHEAFDTFAMLDAWGGPWVSARTFSK
Sbjct: 181 NNPTGNALKAADFQAILAATPRSTVVFVDEAYREYHEAFDTFAMLDAWGGPWVSARTFSK 240

Query: 241 AYGLAGLRMGYGVASSPELVDYLDRIRPPFNVTAVSQAAALAAWEDQDYLKRTVDLTIAE 300
           AYGLAGLRMGYGVASSPELVDYLDRIRPPFNVTAVSQAAALAAWEDQDYLKRTVDLTIAE
Sbjct: 241 AYGLAGLRMGYGVASSPELVDYLDRIRPPFNVTAVSQAAALAAWEDQDYLKRTVDLTIAE 300

Query: 301 RGRVEAVLDDMGVEHTESHANFVFLRSPAGPEATAAHLLHQGLIIRPTPVAGGWVRITIG 360
           RGRVEAVLDDMGVEHTESHANFVFLRSPAGPEATAAHLLHQGLIIRPTPVAGGWVRITIG
Sbjct: 301 RGRVEAVLDDMGVEHTESHANFVFLRSPAGPEATAAHLLHQGLIIRPTPVAGGWVRITIG 360

Query: 361 RPADNDALIAALPAALSL 378
           RPADNDALIAALPAALSL
Sbjct: 361 RPADNDALIAALPAALSL 378


Lambda     K      H
   0.320    0.135    0.403 

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: 646
Number of extensions: 6
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: 378
Length of database: 378
Length adjustment: 30
Effective length of query: 348
Effective length of database: 348
Effective search space:   121104
Effective search space used:   121104
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: 50 (23.9 bits)

Align candidate CCNA_02617 CCNA_02617 (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.16421.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.1e-88  283.4   0.0    1.2e-88  283.3   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02617  CCNA_02617 histidinol-phosphate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02617  CCNA_02617 histidinol-phosphate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.3   0.0   1.2e-88   1.2e-88       1     346 [.      23     372 ..      23     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 283.3 bits;  conditional E-value: 1.2e-88
                             TIGR01141   1 rekikklepYqpg......arelgekevvkLnsnEnPfgpsekvkealkeelkklhrYpdpqalelkealaky 67 
                                           r+ ++ ++ Y++g      ar++g +++ kL+snEn +gps+kv ea+ +++++ h Ypdp++  l++a+ ++
  lcl|FitnessBrowser__Caulo:CCNA_02617  23 RQALEGVQGYKAGmtlaeaARRTGLSAFSKLASNENLLGPSPKVAEAVMAAMAEPHIYPDPHSDVLRAAIGAR 95 
                                           678899999********999***************************************************** PP

                             TIGR01141  68 lgveeenillgnGsdelielliraflepgdavlvleptysmYevsakiagaevkevplkedgqedleavleaa 140
                                           lgv+++ ++++ Gs+ li++++ra+l+pgd++l ++pt+  Ye+  + a+a+++ vp  +++  d++av +aa
  lcl|FitnessBrowser__Caulo:CCNA_02617  96 LGVSPARVVVSPGSEALIDYVFRAVLHPGDSILLSSPTFPTYEIFGRCAEARIIDVPRLANFDIDVPAVCAAA 168
                                           ************************************************************************* PP

                             TIGR01141 141 kekvklvflasPnnPtGnllkreeiekvleev.edalVVvDeAYieFseeasvlellaeyp.nlvvlrTlSKa 211
                                           +  +kl  l++PnnPtGn lk+++++++l+++ ++++V vDeAY e+ e  +++ +l  +    v  rT+SKa
  lcl|FitnessBrowser__Caulo:CCNA_02617 169 ALGPKLLVLCTPNNPTGNALKAADFQAILAATpRSTVVFVDEAYREYHEAFDTFAMLDAWGgPWVSARTFSKA 241
                                           ********************************88*************************99678889****** PP

                             TIGR01141 212 fgLAglRvGyaia.naeiiealekvrapynvsslaleaavaalrdsdkiektveevkkererlleelkklegl 283
                                           +gLAglR+Gy++a ++e++++l+++r+p+nv+ ++++aa+aa +d+d++++tv+  ++er r+++ l ++ g+
  lcl|FitnessBrowser__Caulo:CCNA_02617 242 YGLAGLRMGYGVAsSPELVDYLDRIRPPFNVTAVSQAAALAAWEDQDYLKRTVDLTIAERGRVEAVLDDM-GV 313
                                           ***********98358******************************************************.8* PP

                             TIGR01141 284 evyeSkaNFvlikvkedaeelleallekgiivRdlksaeglleeclRitvGtreenerlleal 346
                                           e  eS+aNFv+++ ++  e+ + +ll++g+i+R    a     +++Rit+G + +n++l++al
  lcl|FitnessBrowser__Caulo:CCNA_02617 314 EHTESHANFVFLRSPAGPEATAAHLLHQGLIIRPTPVA----GGWVRITIGRPADNDALIAAL 372
                                           ***************9999999************9855....579***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (378 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: 10.46
//
[ok]

This GapMind analysis is from Apr 09 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