Alignments for a candidate for iolE in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolE in Caulobacter crescentus NA1000

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate CCNA_01358 CCNA_01358 myo-inositol catabolism protein IolE

Query= reanno::Smeli:SMc00433
         (300 letters)



>FitnessBrowser__Caulo:CCNA_01358
          Length = 299

 Score =  279 bits (713), Expect = 6e-80
 Identities = 143/300 (47%), Positives = 187/300 (62%), Gaps = 4/300 (1%)

Query: 2   IRYGTNPIAWSNDDDHSIGAHLTLEDCLSDCRKIGFDGIEKGHKMPSDPEALKQKLSSYD 61
           IR+G +PIAW NDD   +G    LE  L+DC+ IGF+G+E G   P DP  LK  L  Y 
Sbjct: 3   IRFGVSPIAWINDDMPELGGDTPLESVLADCQAIGFEGVELGGVFPRDPAVLKPLLDRYG 62

Query: 62  LVFVSGWHSTNLLTHDVEAEKKAIQPHLDLLKHNGCKVAIVCETSNAIHGDDSKSLVKDK 121
           L  V GW+S NLL H  E E  A+QPHL LLK  GC V I  ETSNAIHG    +L    
Sbjct: 63  LDLVGGWYSGNLLAHSAEDEIAALQPHLALLKAMGCTVFIHAETSNAIHGARDTAL-SAT 121

Query: 122 PVLPADKWEKFGTDLEAIAEYCAGQGVDLVYHHHMGTIVQTGEEIDLLMRNTGPATKLLL 181
           P L A+ W  FG  L  +A+Y A QG+   YHHH+GT+V+  ++++  +  TGP+  L +
Sbjct: 122 PRLDAEGWTLFGARLTKVADYIAAQGLKFAYHHHLGTVVERPQDLEAFLGATGPSVGLTV 181

Query: 182 DTGHAWFGGSDPAEVARKYMGRVRHIHCKNVRPAV-RKVVEGEGLSFLEGVRRGVFTVPG 240
           DTGHA  GG DP  + R +  RV H+HCK+VR  V + V+  +G SFL+GV  G+FTVPG
Sbjct: 182 DTGHAALGGVDPVALIRAHPERVAHVHCKDVRREVFQSVIGQKGGSFLDGVLAGMFTVPG 241

Query: 241 DEEGGVDFLPVLKTAAEHGYDGWLVIEAEQDSAVRNPFEYQSLGLKSLKTFAREAGLDRA 300
           D  GG+D+  V++  AE  Y GW+++EAEQD A+ NP +Y  +GL +LK  A   GL  A
Sbjct: 242 D--GGLDYAAVMQALAEINYSGWIIVEAEQDPAIANPRQYGEMGLATLKKEAAATGLRAA 299


Lambda     K      H
   0.318    0.137    0.420 

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: 308
Number of extensions: 19
Number of successful extensions: 4
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: 300
Length of database: 299
Length adjustment: 27
Effective length of query: 273
Effective length of database: 272
Effective search space:    74256
Effective search space used:    74256
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate CCNA_01358 CCNA_01358 (myo-inositol catabolism protein IolE)
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.29988.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-118  380.4   0.0   3.9e-118  380.2   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01358  CCNA_01358 myo-inositol cataboli


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01358  CCNA_01358 myo-inositol catabolism protein IolE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.2   0.0  3.9e-118  3.9e-118       2     288 ..       3     289 ..       2     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 380.2 bits;  conditional E-value: 3.9e-118
                             TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalll 74 
                                           +++g++PiaW+ndD+pelggdt+le+vl++++++gf+g+Elg  fp+dpavLk++l+++gl+lv+gw+s++ll
  lcl|FitnessBrowser__Caulo:CCNA_01358   3 IRFGVSPIAWINDDMPELGGDTPLESVLADCQAIGFEGVELGGVFPRDPAVLKPLLDRYGLDLVGGWYSGNLL 75 
                                           89*********************************************************************** PP

                             TIGR04379  75 eksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpklteeeweelaeklnklgeilkekgl 147
                                           ++s+e+ei+a++ hl+llka+g++v++ aE++++i+g +dt+l+  p+l++e w+ ++++l+k++++++ +gl
  lcl|FitnessBrowser__Caulo:CCNA_01358  76 AHSAEDEIAALQPHLALLKAMGCTVFIHAETSNAIHGARDTALSATPRLDAEGWTLFGARLTKVADYIAAQGL 148
                                           ************************************************************************* PP

                             TIGR04379 148 klayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevleev 220
                                           k+ayHhHlgtvve+ ++++ ++ +t+p+ vgl+ DtGH++++g dp+a+++ + +R+ahvH+KDvR+ev+++v
  lcl|FitnessBrowser__Caulo:CCNA_01358 149 KFAYHHHLGTVVERPQDLEAFLGATGPS-VGLTVDTGHAALGGVDPVALIRAHPERVAHVHCKDVRREVFQSV 220
                                           ****************************.******************************************98 PP

                             TIGR04379 221 r.kekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkylee 288
                                             ++  sFld+vl+G+ftvPGdG +d++++++al++ +Y+GW++vEaEqDPa+a+p +y +++  +l++
  lcl|FitnessBrowser__Caulo:CCNA_01358 221 IgQKGGSFLDGVLAGMFTVPGDGGLDYAAVMQALAEINYSGWIIVEAEQDPAIANPRQYGEMGLATLKK 289
                                           625678**********************************************************99987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 10.49
//
[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