Alignments for a candidate for hutI in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Halomonas desiderata SP1

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate WP_086509681.1 BZY95_RS09395 imidazolonepropionase

Query= reanno::MR1:199292
         (408 letters)



>NCBI__GCF_002151265.1:WP_086509681.1
          Length = 406

 Score =  427 bits (1098), Expect = e-124
 Identities = 227/403 (56%), Positives = 283/403 (70%), Gaps = 8/403 (1%)

Query: 6   VWIDVNVATMDPSISAPYGAITHAAIAVKDGKIAWLGPRSELPAFDVLSIPVYRGKGGWI 65
           VW DV +     ++  P       A+ V    I  + P  EL   +        G+GG +
Sbjct: 10  VWHDVTLFDGHDTLPEPM------AVIVAGDTIERVVPMRELDPNETADCQPL-GQGGVM 62

Query: 66  TPGLIDAHTHLVFAGNRANEFELRLKGATYEEIARAGGGIISTVNACREADEAALFELGR 125
           TPGL+D HTHLVF G+RA+EFE RL+GA+YEEIAR GGGI+STV A REA EA LF L R
Sbjct: 63  TPGLVDCHTHLVFGGSRADEFERRLEGASYEEIARRGGGILSTVRATREASEAQLFSLAR 122

Query: 126 QRLNALAKEGVTTVEIKSGYGLDTETELKILRVARELGKHHHVDVKTTFLGAHAVPPEYK 185
            RL AL +EGVTTVEIKSGYGL    ELK+LRVAR LG+   V V TT LGAHA+PPEYK
Sbjct: 123 PRLEALMREGVTTVEIKSGYGLSVADELKMLRVARHLGETLPVRVVTTLLGAHALPPEYK 182

Query: 186 GNSDGYVDLIINKMLPAVIKENLADAVDVFCENIAFNLEQTERVLSAAKAAGLQVKLHAE 245
            +SDGY++L+  +M+PA  ++ LADAVDVFCE IAF++ Q ERV  AA+A GL +K HAE
Sbjct: 183 DDSDGYIELVCREMIPAAAEQGLADAVDVFCEKIAFSVAQCERVFEAAEAHGLPIKAHAE 242

Query: 246 QLSNMGGSELAARLGAKSVDHIEYLDEAGVKALSESGTCAVLLPGAFYFLRETQKPPIDL 305
           QLSN+GGS +AAR GA S DHIEYLDE GV AL E+G+ AVLLPGAF+ LRETQ PPI  
Sbjct: 243 QLSNLGGSAMAARHGALSADHIEYLDEQGVNALREAGSVAVLLPGAFHTLRETQLPPIAA 302

Query: 306 LRQYGVPMVLASDFNPGSFPICSTLLMLNMGCTLFRLTPEEALAGLTLNAAKALGIEDK- 364
           LR+ GVPM +A+D NPGS P+    LMLN  CTLFRLTP EALAG+T + A+ALG+  + 
Sbjct: 303 LREAGVPMAIATDANPGSSPLFMPTLMLNFACTLFRLTPREALAGMTAHGARALGLHTRQ 362

Query: 365 VGSLVVGKQADFCLWNIATPAQLAYSYGVNPCKDVVKNGKLVH 407
           +G +V G  AD CLW++ +PA+LAY+      +  + +G++ H
Sbjct: 363 LGRIVPGAPADLCLWDVESPAELAYAVQPGRLRQRMFSGEITH 405


Lambda     K      H
   0.319    0.136    0.402 

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: 444
Number of extensions: 14
Number of successful extensions: 3
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: 408
Length of database: 406
Length adjustment: 31
Effective length of query: 377
Effective length of database: 375
Effective search space:   141375
Effective search space used:   141375
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_086509681.1 BZY95_RS09395 (imidazolonepropionase)
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))

# 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.carbon/TIGR01224.hmm
# target sequence database:        /tmp/gapView.1219.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01224  [M=377]
Accession:   TIGR01224
Description: hutI: imidazolonepropionase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-144  466.0   0.0   4.6e-144  465.8   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509681.1  BZY95_RS09395 imidazolonepropion


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509681.1  BZY95_RS09395 imidazolonepropionase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8   0.0  4.6e-144  4.6e-144       2     377 .]      25     403 ..      24     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 4.6e-144
                                 TIGR01224   2 edaailveegkiaaigqkaalpgeeaakii.dleGklvvPGlvDpHtHlvfagdRvkefelklqGasYl 69 
                                               e  a++v ++ i  + +  +l ++e a      +G++++PGlvD+HtHlvf+g+R++efe +l+GasY+
  lcl|NCBI__GCF_002151265.1:WP_086509681.1  25 EPMAVIVAGDTIERVVPMRELDPNETADCQpLGQGGVMTPGLVDCHTHLVFGGSRADEFERRLEGASYE 93 
                                               5679**************9999976555440458*********************************** PP

                                 TIGR01224  70 eilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkee 138
                                               ei+++GgGilstvratr+Ase++l+  a++rl+ l+r+G+tt+E+KsGYGL + +ElkmLrv+++l e+
  lcl|NCBI__GCF_002151265.1:WP_086509681.1  94 EIARRGGGILSTVRATREASEAQLFSLARPRLEALMREGVTTVEIKSGYGLSVADELKMLRVARHLGET 162
                                               ********************************************************************* PP

                                 TIGR01224 139 lpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaq 207
                                               lpv+vvtt+lgaHa+P+e+++d+d y++ ++ e+ip++ae+ la+avDvFcek +Fsv+q +r+++aa+
  lcl|NCBI__GCF_002151265.1:WP_086509681.1 163 LPVRVVTTLLGAHALPPEYKDDSDGYIELVCREMIPAAAEQGLADAVDVFCEKIAFSVAQCERVFEAAE 231
                                               ********************************************************************* PP

                                 TIGR01224 208 eaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaappa 275
                                               ++Gl++k Hae+l++lgg+++aa+ ga+sadH+e++++++++al eag+vavlLPg++++Lr ++ pp+
  lcl|NCBI__GCF_002151265.1:WP_086509681.1 232 AHGLPIKAHAEQLSNLGGSAMAARHGALSADHIEYLDEQGVNALREAGSVAVLLPGAFHTLReTQLPPI 300
                                               **************************************************************9999*** PP

                                 TIGR01224 276 rklidekvivalatDlnPgsspllslqlilslavtllkltaeealaaatvnaAqalglg.eekGtleeG 343
                                                +l++++v++a+atD+nPgsspl   +l+l++a+tl++lt+ eala++t++ A algl   + G +  G
  lcl|NCBI__GCF_002151265.1:WP_086509681.1 301 AALREAGVPMAIATDANPGSSPLFMPTLMLNFACTLFRLTPREALAGMTAHGARALGLHtRQLGRIVPG 369
                                               *********************************************************996778****** PP

                                 TIGR01224 344 kdadlvvlsaesyeeiaYrlgvnvveaviknGev 377
                                                 adl ++++es++e+aY +   ++ ++++ Ge+
  lcl|NCBI__GCF_002151265.1:WP_086509681.1 370 APADLCLWDVESPAELAYAVQPGRLRQRMFSGEI 403
                                               **********************9******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (406 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: 8.01
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources