Alignments for a candidate for hutI in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Marinomonas arctica 328

Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate WP_111607196.1 DK187_RS09540 imidazolonepropionase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_317
         (401 letters)



>NCBI__GCF_003259225.1:WP_111607196.1
          Length = 426

 Score =  530 bits (1366), Expect = e-155
 Identities = 266/399 (66%), Positives = 319/399 (79%), Gaps = 1/399 (0%)

Query: 1   MKTLWQHCHVATMAQGVYSIIEDAAIVTSGAHIEWIGPRGELPAGEYPAVNDLNGAWVTP 60
           + ++W+  HVATM  G YSIIE+AAI   G  I WIG   +LPA +    +DL G W+TP
Sbjct: 9   LDSVWRGAHVATMKGGQYSIIENAAIGVRGGRIVWIGKAHDLPAYQTQHEHDLGGGWITP 68

Query: 61  GLIDCHTHTVFGGNRSGEFEQRLQGVSYADIAASGGGIASTVRATRAASEDELFASAAKR 120
           GLIDCHTH VFGGNR+GEFEQRL GVSY DIA  GGGIAS+VRATR ASE EL ASA +R
Sbjct: 69  GLIDCHTHLVFGGNRAGEFEQRLNGVSYQDIAKQGGGIASSVRATREASEAELVASALRR 128

Query: 121 LKSLMRDGVTSIEIKSGYGLDLANERKMLRVARRLGAELPVSVRSTCLAAHALPPEYKDR 180
           LKSLM DGVT++EIKSGYGL L +E KMLRVA +LG E PV+++ TCLAAHA+PPE+ D+
Sbjct: 129 LKSLMADGVTTVEIKSGYGLSLDSELKMLRVAGKLGDEWPVTIKRTCLAAHAMPPEFDDK 188

Query: 181 ADDYIDHICADMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQALGLPVKLHAEQL 240
            D YID++C  +LP +A  G+ DAVDAFCE +AFS  QV R F TA++LGLPVK+HAEQL
Sbjct: 189 -DAYIDYLCEKVLPKVAQLGMADAVDAFCEGIAFSTEQVARYFRTAESLGLPVKIHAEQL 247

Query: 241 SSLHGSSLAARYHALSADHLEFMTEDDAIAMAKSGTVAVLLPGAFYFLRETQLPPMEALR 300
           SSL G+++A+ + ALSADH+EF+ E D  AMA+SGTVAVLLPGAF+ L+ETQ PP+  LR
Sbjct: 248 SSLGGTAMASSFKALSADHIEFIEESDVKAMAESGTVAVLLPGAFFTLKETQRPPIALLR 307

Query: 301 KHGVKIAIASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGATIHAATALGMADTHGS 360
           ++GV +AIA+D NPGTSPALSLRLM+NMACT F +TPEEALAGATIHAA ALGMAD+HGS
Sbjct: 308 QYGVPMAIATDANPGTSPALSLRLMMNMACTLFALTPEEALAGATIHAAKALGMADSHGS 367

Query: 361 LEVGKVADFVAWQIDRPADLCYWLGGDLEKRVVRHGVES 399
           LE+GKVADFV WQ+D P +L YWLGGDL K  V  G +S
Sbjct: 368 LEIGKVADFVCWQVDSPGELSYWLGGDLVKTRVYEGKQS 406


Lambda     K      H
   0.320    0.133    0.399 

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: 502
Number of extensions: 16
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: 401
Length of database: 426
Length adjustment: 31
Effective length of query: 370
Effective length of database: 395
Effective search space:   146150
Effective search space used:   146150
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 WP_111607196.1 DK187_RS09540 (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.2018768.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-155  502.8   0.0   3.1e-155  502.6   0.0    1.0  1  NCBI__GCF_003259225.1:WP_111607196.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003259225.1:WP_111607196.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  502.6   0.0  3.1e-155  3.1e-155       1     376 [.      29     404 ..      29     405 .. 0.99

  Alignments for each domain:
  == domain 1  score: 502.6 bits;  conditional E-value: 3.1e-155
                             TIGR01224   1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleila 73 
                                           ie+aai v++g+i++ig+  +lp+++ ++++dl+G+ ++PGl+D+HtHlvf+g+R+ efe++l+G+sY++i++
  NCBI__GCF_003259225.1:WP_111607196.1  29 IENAAIGVRGGRIVWIGKAHDLPAYQTQHEHDLGGGWITPGLIDCHTHLVFGGNRAGEFEQRLNGVSYQDIAK 101
                                           5899********************************************************************* PP

                             TIGR01224  74 eGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvtt 146
                                           +GgGi s vratr+Ase+el+++a  rlk+l++ G+tt+E+KsGYGL l++ElkmLrv+ +l +e pv ++ t
  NCBI__GCF_003259225.1:WP_111607196.1 102 QGGGIASSVRATREASEAELVASALRRLKSLMADGVTTVEIKSGYGLSLDSELKMLRVAGKLGDEWPVTIKRT 174
                                           ************************************************************************* PP

                             TIGR01224 147 flgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaee 219
                                           +l+aHa+P+e++++ d+y+d ++e+++pkva+  +a+avD+Fce  +Fs eq+ r+++ a+  Gl+vk+Hae+
  NCBI__GCF_003259225.1:WP_111607196.1 175 CLAAHAMPPEFDDK-DAYIDYLCEKVLPKVAQLGMADAVDAFCEGIAFSTEQVARYFRTAESLGLPVKIHAEQ 246
                                           **********9988.********************************************************** PP

                             TIGR01224 220 lkalggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLr.eaapparklidekvivalatDl 291
                                           l++lgg+++a++++a+sadH+e ++++d+ka+ae+gtvavlLPg++f+L+ ++ pp+  l++++v++a+atD+
  NCBI__GCF_003259225.1:WP_111607196.1 247 LSSLGGTAMASSFKALSADHIEFIEESDVKAMAESGTVAVLLPGAFFTLKeTQRPPIALLRQYGVPMAIATDA 319
                                           **************************************************9999******************* PP

                             TIGR01224 292 nPgsspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlg 364
                                           nPg+sp lsl+l++++a+tl+ lt+eeala+at++aA+alg+++++G+le Gk ad+v ++++s+ e++Y+lg
  NCBI__GCF_003259225.1:WP_111607196.1 320 NPGTSPALSLRLMMNMACTLFALTPEEALAGATIHAAKALGMADSHGSLEIGKVADFVCWQVDSPGELSYWLG 392
                                           ************************************************************************* PP

                             TIGR01224 365 vnvveaviknGe 376
                                           ++ v++++ +G+
  NCBI__GCF_003259225.1:WP_111607196.1 393 GDLVKTRVYEGK 404
                                           ********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (426 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.03
//
[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 2024 update 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