Alignments for a candidate for iolE in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Beijerinckia indica ATCC 9039

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate WP_012385755.1 BIND_RS14295 myo-inosose-2 dehydratase

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



>NCBI__GCF_000019845.1:WP_012385755.1
          Length = 310

 Score =  268 bits (686), Expect = 9e-77
 Identities = 138/287 (48%), Positives = 176/287 (61%), Gaps = 2/287 (0%)

Query: 7   RIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSLLAQYDL 66
           ++GI P++W NDDLP LGG+T LE  L E R  G+ G E G KFP+    L   LA + L
Sbjct: 4   KLGIAPIAWSNDDLPELGGQTSLETCLRESRAAGFSGVETGGKFPKTAAELGPKLAAFGL 63

Query: 67  ALVSGWYSGRL--ARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGAAQPLYQRP 124
           +L SGWYSG +  A   +  E  +    L+L  + GA  + YGE A +IQ          
Sbjct: 64  SLASGWYSGTVLDAPDDLAAEKEKAASQLQLFRELGAACLAYGETAGTIQNKRTAPLNSR 123

Query: 125 RFFSEKQWADYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDAVGLLF 184
           R  +E Q   Y  R+  FA Y   +GV L +HHHMG  +ET  D+D LM  T +AVGLL+
Sbjct: 124 RRLAEDQIRTYGHRLTRFAEYCSEKGVPLGFHHHMGTGIETEEDLDLLMRHTGEAVGLLY 183

Query: 185 DAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFTVPGD 244
           D GH+ FAGGD L V++KH  R+ HVH KDVR  V+      + SFLDAV+AGAFTVPGD
Sbjct: 184 DTGHMRFAGGDHLRVIEKHGRRIIHVHAKDVRDQVISSLDRSHDSFLDAVLAGAFTVPGD 243

Query: 245 GAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQKGYKTLRA 291
           G+++F A+ +RL   GY GW +VEAEQDPV AP  EYA  GY+ L A
Sbjct: 244 GSIDFNAVAQRLSDVGYQGWFIVEAEQDPVKAPPAEYAVIGYRALSA 290


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: 280
Number of extensions: 11
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: 310
Length adjustment: 27
Effective length of query: 278
Effective length of database: 283
Effective search space:    78674
Effective search space used:    78674
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 WP_012385755.1 BIND_RS14295 (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.675873.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-120  387.5   0.0   2.6e-120  387.3   0.0    1.0  1  NCBI__GCF_000019845.1:WP_012385755.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000019845.1:WP_012385755.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.3   0.0  2.6e-120  2.6e-120       2     288 ..       3     290 ..       2     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.3 bits;  conditional E-value: 2.6e-120
                             TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalll 74 
                                           +klgiaPiaW+ndDlpelgg+t+le++l+e ++agfsg+E+g kfpk++a+L ++l  +gl+l+sgw+s+++l
  NCBI__GCF_000019845.1:WP_012385755.1   3 AKLGIAPIAWSNDDLPELGGQTSLETCLRESRAAGFSGVETGGKFPKTAAELGPKLAAFGLSLASGWYSGTVL 75 
                                           59*********************************************************************99 PP

                             TIGR04379  75 ..eksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpklteeeweelaeklnklgeilkek 145
                                              +++++e+e+ +++l+l+++lga+++ ++E++++iq+++++pl++r++l e+++++++++l++++e+++ek
  NCBI__GCF_000019845.1:WP_012385755.1  76 daPDDLAAEKEKAASQLQLFRELGAACLAYGETAGTIQNKRTAPLNSRRRLAEDQIRTYGHRLTRFAEYCSEK 148
                                           6667899****************************************************************** PP

                             TIGR04379 146 glklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevle 218
                                           g++l +HhH+gt++etee++d lm +t+++ vgllyDtGH+ fag+d l+v+ek+++Ri hvH+KDvR +v++
  NCBI__GCF_000019845.1:WP_012385755.1 149 GVPLGFHHHMGTGIETEEDLDLLMRHTGEA-VGLLYDTGHMRFAGGDHLRVIEKHGRRIIHVHAKDVRDQVIS 220
                                           ****************************99.****************************************** PP

                             TIGR04379 219 evrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkylee 288
                                           +++++++sFldavl+G+ftvPGdG+idf+++++ l+  +Y+GW++vEaEqDP ka+p eya ++++ l++
  NCBI__GCF_000019845.1:WP_012385755.1 221 SLDRSHDSFLDAVLAGAFTVPGDGSIDFNAVAQRLSDVGYQGWFIVEAEQDPVKAPPAEYAVIGYRALSA 290
                                           *****************************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (310 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.44
//
[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