Alignments for a candidate for hutI in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutI in Flavobacterium beibuense F44-8

Align Imidazolonepropionase; EC 3.5.2.7; Imidazolone-5-propionate hydrolase (uncharacterized)
to candidate WP_035133672.1 Q763_RS09775 imidazolonepropionase

Query= curated2:A0LZE0
         (411 letters)



>NCBI__GCF_000769915.1:WP_035133672.1
          Length = 412

 Score =  596 bits (1536), Expect = e-175
 Identities = 291/411 (70%), Positives = 353/411 (85%)

Query: 1   MTLLVTNIKELLQVREQNILKVSGSEMKELPTIKNAWLLIENDKIADFGTMKNMPKITAD 60
           M +L+TNIKELLQVRE  I KVSG +M  LP+++NA+LLIEN+ IAD+GTM+N P  +  
Sbjct: 1   MKILITNIKELLQVREDGIEKVSGKDMAVLPSLQNAYLLIENNIIADYGTMENCPATSGI 60

Query: 61  QTIDATGKIVLPTWCDSHTHIVYAGNREQEFADRINGLSYEEIANRGGGILNSVKTLQDT 120
           QTIDATGK VLP+WCDSHTHIVYAGNREQEF DRINGLSYEEIA+RGGGILNS K L +T
Sbjct: 61  QTIDATGKTVLPSWCDSHTHIVYAGNREQEFVDRINGLSYEEIASRGGGILNSAKKLNET 120

Query: 121 SEEEVYEQSAKRLKEVMKLGTGAVEIKSGYGLTEKAELKMLRVIKKLRENYDLPVKSTFL 180
           SEE++Y QS  RL+EVM+ GTGAVEIKSGYGLT + ELKMLRVIK+LRE Y + +K+TFL
Sbjct: 121 SEEDLYLQSRTRLEEVMQQGTGAVEIKSGYGLTVEGELKMLRVIKRLREEYPIAIKATFL 180

Query: 181 GAHAIPKEYKNDPDAYMDLVINEILPKVAKEGLAEYIDIFCEKGYFSIKDTHRLLSAAKE 240
           GAHA P EYK +  AY+DL+INE+LPK+A+E LA+YID F E GYFS+++T R++ A K+
Sbjct: 181 GAHAFPAEYKENHSAYIDLIINEMLPKIAEEKLADYIDAFLETGYFSVEETERIMEAGKK 240

Query: 241 HGLKPKIHVNQFNSIGGVKVGVEHEALSVDHLEVMNDEDIEVLKGTRTMPVALPSCSLFL 300
           +GL+ KIHVNQF +I G++  V+++ALSVDHLE++ DEDIEVLK T+TMPVALP+CS F+
Sbjct: 241 YGLQAKIHVNQFTAIKGIEACVKYDALSVDHLEIVTDEDIEVLKDTKTMPVALPTCSFFI 300

Query: 301 SIPYTPARKILDAELPLALATDFNPGSTPSGNMNLVVSLACIKMKMTPEEAINAATINGA 360
           SIPYTPARK+++A LPLALATDFNPG+TPSGNMNLVV+ ACIKMKMTPEEAINAATINGA
Sbjct: 301 SIPYTPARKMMEAGLPLALATDFNPGTTPSGNMNLVVATACIKMKMTPEEAINAATINGA 360

Query: 361 YAMDLSETHGSITKGKMANFMITKEIPSFTFLPYAFGTNSIDSVYINGKLI 411
           YAMDLS+THGSITKGK AN +ITK + S+  LPYAFG+N ID+V + GK+I
Sbjct: 361 YAMDLSKTHGSITKGKRANLIITKPLTSYYQLPYAFGSNLIDTVIVEGKVI 411


Lambda     K      H
   0.315    0.133    0.376 

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: 558
Number of extensions: 8
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: 411
Length of database: 412
Length adjustment: 31
Effective length of query: 380
Effective length of database: 381
Effective search space:   144780
Effective search space used:   144780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_035133672.1 Q763_RS09775 (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.459389.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-130  421.0   0.3   2.2e-130  420.8   0.3    1.0  1  NCBI__GCF_000769915.1:WP_035133672.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035133672.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.8   0.3  2.2e-130  2.2e-130       3     377 .]      35     410 ..      33     410 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.8 bits;  conditional E-value: 2.2e-130
                             TIGR01224   3 daailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklqGasYleilaeG 75 
                                           +a +l+e++ ia  g   + p++ + ++id++Gk+v+P   D+HtH+v+ag+R++ef  +++G sY+ei+ +G
  NCBI__GCF_000769915.1:WP_035133672.1  35 NAYLLIENNIIADYGTMENCPATSGIQTIDATGKTVLPSWCDSHTHIVYAGNREQEFVDRINGLSYEEIASRG 107
                                           67899******************************************************************** PP

                             TIGR01224  76 gGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkmLrvikalkeelpvdvvttfl 148
                                           gGil   ++  + see+l  + ++rl++++++Gt ++E+KsGYGL++e+ElkmLrvik+l+ee p+ +++tfl
  NCBI__GCF_000769915.1:WP_035133672.1 108 GGILNSAKKLNETSEEDLYLQSRTRLEEVMQQGTGAVEIKSGYGLTVEGELKMLRVIKRLREEYPIAIKATFL 180
                                           ************************************************************************* PP

                             TIGR01224 149 gaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekgvFsveqsrrilkaaqeaGlavklHaeelk 221
                                           gaHa P e++e++ +y+d i++e++pk+aeekla+++D+F e+g Fsve+++ri++a+++ Gl++k+H ++++
  NCBI__GCF_000769915.1:WP_035133672.1 181 GAHAFPAEYKENHSAYIDLIINEMLPKIAEEKLADYIDAFLETGYFSVEETERIMEAGKKYGLQAKIHVNQFT 253
                                           ************************************************************************* PP

                             TIGR01224 222 alggaelaaklgavsadHleeasdedikalaeagtvavlLPgtaflLreaapparklidekvivalatDlnPg 294
                                           a+ g e   k +a+s+dHle ++dedi+ l+++ t++v LP+  f++   ++park+++++ ++alatD+nPg
  NCBI__GCF_000769915.1:WP_035133672.1 254 AIKGIEACVKYDALSVDHLEIVTDEDIEVLKDTKTMPVALPTCSFFISIPYTPARKMMEAGLPLALATDFNPG 326
                                           ************************************************************************* PP

                             TIGR01224 295 sspllslqlilslavtllkltaeealaaatvnaAqalglgeekGtleeGkdadlvvls.aesyeeiaYrlgvn 366
                                           ++p  +++l+++ a+ ++k+t+eea++aat+n A+a++l++++G++++Gk+a+l++ + ++sy +++Y +g n
  NCBI__GCF_000769915.1:WP_035133672.1 327 TTPSGNMNLVVATACIKMKMTPEEAINAATINGAYAMDLSKTHGSITKGKRANLIITKpLTSYYQLPYAFGSN 399
                                           ******************************************************9985489************ PP

                             TIGR01224 367 vveaviknGev 377
                                            +++vi++G+v
  NCBI__GCF_000769915.1:WP_035133672.1 400 LIDTVIVEGKV 410
                                           *********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (377 nodes)
Target sequences:                          1  (412 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: 24.76
//
[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