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 Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate BWI76_RS10210 BWI76_RS10210 endonuclease

Query= reanno::BFirm:BPHYT_RS13920
         (305 letters)



>FitnessBrowser__Koxy:BWI76_RS10210
          Length = 298

 Score =  231 bits (590), Expect = 1e-65
 Identities = 129/282 (45%), Positives = 163/282 (57%), Gaps = 4/282 (1%)

Query: 6   VRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSLLAQYD 65
           + +G++PLSW ND L  LGG  PLE  L E  E GY+G ELG KFPR    L  +L Q  
Sbjct: 7   IHVGVSPLSWTNDVLEDLGGYIPLETCLAEAAEAGYEGIELGRKFPRTIDTLAPVLNQAK 66

Query: 66  LALVSGWYSGRLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVA--DSIQGAAQPLYQR 123
           L L SGWY+G LA+RS E+E+A V  H  LL   GA  MVYGE      +    +PL + 
Sbjct: 67  LKLASGWYNGLLAKRSFEDELAAVHDHAMLLKSLGAKVMVYGECGAMPGLTPLDEPLSKS 126

Query: 124 PRFFSEKQWADYAARVDEFARYTLSR-GVRLAYHHHMGAYVETPADVDQLMARTSDAVGL 182
           P      +   YA +V+  A   L   G+RLAYHHH+   VET  ++   +  T+D VG+
Sbjct: 127 PPL-GHIELPQYAEKVNNLAVSLLKNYGLRLAYHHHLMMVVETDDELKAFLKATNDLVGI 185

Query: 183 LFDAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFTVP 242
             D GH T AG D   VL+ +  RV HVH KDVR  V+    N N SF +AV AG FTVP
Sbjct: 186 ALDCGHATVAGVDINWVLENYGNRVAHVHLKDVRGEVLNNVINNNLSFNNAVRAGLFTVP 245

Query: 243 GDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQK 284
           G+G VN+  +I  LK   Y GW+++EAEQDP  AP  E  +K
Sbjct: 246 GEGIVNYAPVIHFLKNSTYEGWIIIEAEQDPEKAPPLETVKK 287


Lambda     K      H
   0.320    0.137    0.417 

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: 6
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: 305
Length of database: 298
Length adjustment: 27
Effective length of query: 278
Effective length of database: 271
Effective search space:    75338
Effective search space used:    75338
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_RS10210 BWI76_RS10210 (endonuclease)
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.15207.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     1e-100  323.0   0.0   1.1e-100  322.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS10210  BWI76_RS10210 endonuclease


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS10210  BWI76_RS10210 endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.9   0.0  1.1e-100  1.1e-100       2     288 ..       7     294 ..       6     296 .. 0.96

  Alignments for each domain:
  == domain 1  score: 322.9 bits;  conditional E-value: 1.1e-100
                               TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsal 72 
                                             +++g++P++W+nd l++lgg ++le++l+eaaeag++g+Elg+kfp++ ++L+++l++ +l+l+sgw+ +l
  lcl|FitnessBrowser__Koxy:BWI76_RS10210   7 IHVGVSPLSWTNDVLEDLGGYIPLETCLAEAAEAGYEGIELGRKFPRTIDTLAPVLNQAKLKLASGWYNGL 77 
                                             789******************************************************************** PP

                               TIGR04379  73 lleksveeeieavrehlellkalgakvivvaEvgksiqgdk.dtplaerpklteeeweelaeklnklge.i 141
                                             l+++s+e+e++av++h+ llk+lgakv+v++E+g     ++ d+pl++ p l + e+ ++aek+n+l+  +
  lcl|FitnessBrowser__Koxy:BWI76_RS10210  78 LAKRSFEDELAAVHDHAMLLKSLGAKVMVYGECGAMPGLTPlDEPLSKSPPLGHIELPQYAEKVNNLAVsL 148
                                             *********************************9887665437889999******************9626 PP

                               TIGR04379 142 lkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDv 212
                                             lk++gl+layHhHl  vvet +e++ ++++t++  vg+ +D GH+++ag d   vle+y++R+ahvHlKDv
  lcl|FitnessBrowser__Koxy:BWI76_RS10210 149 LKNYGLRLAYHHHLMMVVETDDELKAFLKATNDL-VGIALDCGHATVAGVDINWVLENYGNRVAHVHLKDV 218
                                             789****************************976.************************************ PP

                               TIGR04379 213 RkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkak 283
                                             R evl++v +++ sF +av++G+ftvPG+G ++++++++ lk++ YeGW+++EaEqDP+ka+ple  kka+
  lcl|FitnessBrowser__Koxy:BWI76_RS10210 219 RGEVLNNVINNNLSFNNAVRAGLFTVPGEGIVNYAPVIHFLKNSTYEGWIIIEAEQDPEKAPPLETVKKAR 289
                                             **********************************************************************9 PP

                               TIGR04379 284 kylee 288
                                               +++
  lcl|FitnessBrowser__Koxy:BWI76_RS10210 290 AWVKS 294
                                             98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (298 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: 6.57
//
[ok]

This GapMind analysis is from Sep 17 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