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.7365.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.26
//
[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:

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:

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:

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:

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