Alignments for a candidate for iolE in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Klebsiella michiganensis M5al

Align Inosose dehydratase; 2-keto-myo-inositol dehydratase; 2KMI dehydratase; EC 4.2.1.44 (characterized)
to candidate BWI76_RS03105 BWI76_RS03105 myo-inosose-2 dehydratase

Query= SwissProt::P42416
         (297 letters)



>FitnessBrowser__Koxy:BWI76_RS03105
          Length = 299

 Score =  281 bits (720), Expect = 1e-80
 Identities = 141/294 (47%), Positives = 194/294 (65%), Gaps = 6/294 (2%)

Query: 1   MGKNEILWGIAPIGWRNDDMPEIGAGNTLQHLLSDIVVARFQGTEVGGFFP-EPAILNKE 59
           M K+ +   IAPIGW NDDMPE+G+ NT Q ++S++ +A F G+EVG  +P +PA+L   
Sbjct: 1   MNKDNVKLAIAPIGWTNDDMPELGSENTFQQIVSEMALAGFTGSEVGSKYPRDPAVLKPM 60

Query: 60  LKLRNLRIAGKWFSSFILRDGLGEAAKTFTLHCEYLQQVNADVAVVSEQTYSVQSLEKNV 119
           L +R ++I   WFS+F       +    F  H  +L  + A V   SEQ+ S+Q LEK +
Sbjct: 61  LDIRGIQICNAWFSTFFANGQREKTIDEFVNHMNFLHAMGAKVIGCSEQSGSIQGLEKPI 120

Query: 120 FTE-KPHFTDDEWERLCEGLNHLGEIAAQHGLKLVYHHHLGTGVQTAEEVDRLMAGTDPA 178
               KP F+++EW+R+ EG N LG +AA+ G+++  HHH+GTG+QT  E+D+ M+  D  
Sbjct: 121 LENAKPCFSEEEWQRVAEGYNTLGRLAAEKGMQVCLHHHMGTGIQTTAEIDKFMSLVDDK 180

Query: 179 HVHLLYDTGHAYISDGD---YMGMLEKHIGRIKHVHFKDARLNVMEQCRLEGQSFRQSFL 235
            V LLYDTGHA+ S+G     + +L+K++ RI HVH KD R  V+EQ R EG SF     
Sbjct: 181 -VFLLYDTGHAWYSEGGEEPMLAILKKYLPRINHVHLKDVRPPVIEQVRREGLSFLDGVK 239

Query: 236 KGMFTVPGDGCIDFREVYQLLLKHSYSGWIVIEAEQDPDVANPLEYALIARNYI 289
           KG FTVPGDG IDFR V++LL +H Y GW+V+EAEQDP +ANP EYA+ AR YI
Sbjct: 240 KGTFTVPGDGVIDFRPVFKLLDEHGYKGWMVVEAEQDPALANPFEYAVKARKYI 293


Lambda     K      H
   0.321    0.139    0.427 

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: 262
Number of extensions: 15
Number of successful extensions: 5
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: 297
Length of database: 299
Length adjustment: 27
Effective length of query: 270
Effective length of database: 272
Effective search space:    73440
Effective search space used:    73440
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: 48 (23.1 bits)

Align candidate BWI76_RS03105 BWI76_RS03105 (myo-inosose-2 dehydratase)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))

# 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/TIGR04379.hmm
# target sequence database:        /tmp/gapView.10172.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04379  [M=290]
Accession:   TIGR04379
Description: myo_inos_iolE: myo-inosose-2 dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.9e-121  390.5   0.0   3.3e-121  390.3   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS03105  BWI76_RS03105 myo-inosose-2 dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS03105  BWI76_RS03105 myo-inosose-2 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.3   0.0  3.3e-121  3.3e-121       1     289 [.       5     296 ..       5     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 390.3 bits;  conditional E-value: 3.3e-121
                               TIGR04379   1 kvklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsa 71 
                                             +vkl+iaPi W+ndD+pelg+++t++q++se+a agf+g+E+g+k+p+dpavLk++l+ rg+++++ wfs+
  lcl|FitnessBrowser__Koxy:BWI76_RS03105   5 NVKLAIAPIGWTNDDMPELGSENTFQQIVSEMALAGFTGSEVGSKYPRDPAVLKPMLDIRGIQICNAWFST 75 
                                             59********************************************************************* PP

                               TIGR04379  72 llleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaer.pklteeeweelaeklnklgei 141
                                             ++++ ++e++i+++ +h+++l+a+gakvi ++E+++siqg ++  l++  p ++eeew+++ae+ n+lg++
  lcl|FitnessBrowser__Koxy:BWI76_RS03105  76 FFANGQREKTIDEFVNHMNFLHAMGAKVIGCSEQSGSIQGLEKPILENAkPCFSEEEWQRVAEGYNTLGRL 146
                                             ****************************************97777766579******************** PP

                               TIGR04379 142 lkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfa..gedp.lavlekyadRiahvHl 209
                                             ++ekg+++  HhH+gt+++t++eid++m+l d++ v llyDtGH+ ++  ge+p la+l+ky  Ri+hvHl
  lcl|FitnessBrowser__Koxy:BWI76_RS03105 147 AAEKGMQVCLHHHMGTGIQTTAEIDKFMSLVDDK-VFLLYDTGHAWYSegGEEPmLAILKKYLPRINHVHL 216
                                             *********************************9.***********973245552699************* PP

                               TIGR04379 210 KDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyak 280
                                             KDvR+ v+e+vr+e  sFld+v+kG ftvPGdG idf+++++ l++++Y+GW+vvEaEqDPa a+p+eya 
  lcl|FitnessBrowser__Koxy:BWI76_RS03105 217 KDVRPPVIEQVRREGLSFLDGVKKGTFTVPGDGVIDFRPVFKLLDEHGYKGWMVVEAEQDPALANPFEYAV 287
                                             *********************************************************************** PP

                               TIGR04379 281 kakkyleel 289
                                             ka+ky++e+
  lcl|FitnessBrowser__Koxy:BWI76_RS03105 288 KARKYIRET 296
                                             ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (299 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: 9.33
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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