Alignments for a candidate for hisN in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for hisN in Caulobacter crescentus NA1000

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate CCNA_02335 CCNA_02335 inositol monophosphatase family protein

Query= reanno::azobra:AZOBR_RS03845
         (260 letters)



>FitnessBrowser__Caulo:CCNA_02335
          Length = 278

 Score =  201 bits (511), Expect = 1e-56
 Identities = 114/255 (44%), Positives = 157/255 (61%), Gaps = 17/255 (6%)

Query: 19  ASGPVIRQYFRTPVAVDDK-----------ADASPVTIADREAERTIRAIIEAERPDDGI 67
           AS  VI   FR    ++DK           A   PVT ADR AE  IRA+I    PD G+
Sbjct: 21  ASADVILPLFRADHGLEDKGAGKNLPRDTHAAFDPVTEADRGAEAAIRALIAQRFPDHGV 80

Query: 68  YGEEFGTKNLDAEWVWVIDPIDGTKSFITGRPIFGTLIALLHRGRPVLGVIDQPIVRDRW 127
            GEE+G    DAE+VWV+DPIDGT++FI G P++ TLI L H GRPVLG I QP V + +
Sbjct: 81  IGEEYGEDRPDAEFVWVLDPIDGTRAFIAGLPLWTTLIGLRHEGRPVLGSIGQPYVNEIF 140

Query: 128 LGVEGRPTLFNG---QPARVRECAGGLAAATLGTTSPD-LFPGADQDAFRRVAGAAKVSV 183
           +G  G   L +G   +P RVRECA  +  A + TT PD  F GA++ A+ +V  AAK++ 
Sbjct: 141 IGHAGGARLVSGGEARPIRVRECA-NINDAVIATTDPDACFDGAERGAWLQVRAAAKLAR 199

Query: 184 YGGDCYSYGLLAAGYYDLVVESGLKLYDFAALVPVVTGAGGLMTDWDGRPLDATSSGRVV 243
            G D Y+Y ++A G  D+V+E+GLK +D  A +P++ GAGG++T+W G P+   + G++V
Sbjct: 200 LGCDAYAYAMVAMGKMDMVIEAGLKSWDIEAAIPLIEGAGGMVTNWRGEPV-GPNGGQMV 258

Query: 244 AAGDARTHRETLAAL 258
            +GD R   E L +L
Sbjct: 259 ISGDRRPLDEALVSL 273


Lambda     K      H
   0.320    0.139    0.424 

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: 267
Number of extensions: 12
Number of successful extensions: 2
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: 260
Length of database: 278
Length adjustment: 25
Effective length of query: 235
Effective length of database: 253
Effective search space:    59455
Effective search space used:    59455
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: 47 (22.7 bits)

Align candidate CCNA_02335 CCNA_02335 (inositol monophosphatase family protein)
to HMM TIGR02067 (hisN: histidinol-phosphatase (EC 3.1.3.15))

# 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/TIGR02067.hmm
# target sequence database:        /tmp/gapView.23265.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02067  [M=252]
Accession:   TIGR02067
Description: his_9_HisN: histidinol-phosphatase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-103  330.1   0.0   5.2e-103  329.9   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02335  CCNA_02335 inositol monophosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02335  CCNA_02335 inositol monophosphatase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.9   0.0  5.2e-103  5.2e-103       2     251 ..      12     273 ..      11     274 .. 0.98

  Alignments for each domain:
  == domain 1  score: 329.9 bits;  conditional E-value: 5.2e-103
                             TIGR02067   2 lalalelaeaageailkyfrasdlkvdkksdk..........tpVteADraaEeaireliaakfPddgilGEE 64 
                                           +a++l+l++a++++il+ fra++  +dk + k          +pVteADr aE+air+lia++fPd+g++GEE
  lcl|FitnessBrowser__Caulo:CCNA_02335  12 DAFILDLNRASADVILPLFRADHGLEDKGAGKnlprdthaafDPVTEADRGAEAAIRALIAQRFPDHGVIGEE 84 
                                           5899*************************99999*************************************** PP

                             TIGR02067  65 fgeeeedaeyvWvlDPiDGTksFirGvPvwgtLiaLlekgkpvlGvisqPalgerfvaakgegallngge.re 136
                                           +ge+++dae+vWvlDPiDGT++Fi+G+P+w+tLi+L+++g+pvlG i qP+++e+f++++g++ l++gge r+
  lcl|FitnessBrowser__Caulo:CCNA_02335  85 YGEDRPDAEFVWVLDPIDGTRAFIAGLPLWTTLIGLRHEGRPVLGSIGQPYVNEIFIGHAGGARLVSGGEaRP 157
                                           *******************************************************************9777** PP

                             TIGR02067 137 lrvsevaklsdAvlvttspkaledeeereafeklrrkarltryggdcyayalvAsGrvdlvveaelspyDiaa 209
                                           +rv+e+a+++dAv++tt+p+a++d +er a+ ++r++a+l+r+g+d+yaya+vA+G++d+v+ea+l+++Di+a
  lcl|FitnessBrowser__Caulo:CCNA_02335 158 IRVRECANINDAVIATTDPDACFDGAERGAWLQVRAAAKLARLGCDAYAYAMVAMGKMDMVIEAGLKSWDIEA 230
                                           ************************************************************************* PP

                             TIGR02067 210 lipiieeAggvitdwkGkeae.eggeavaaanaalhdevlell 251
                                           +ip+ie+Agg++t+w+G+++  +gg++v++++++  de+l +l
  lcl|FitnessBrowser__Caulo:CCNA_02335 231 AIPLIEGAGGMVTNWRGEPVGpNGGQMVISGDRRPLDEALVSL 273
                                           ********************99*****************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (252 nodes)
Target sequences:                          1  (278 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: 4.76
//
[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