GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolE in Herbaspirillum seropedicae SmR1

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate HSERO_RS12135 HSERO_RS12135 xylose isomerase

Query= reanno::HerbieS:HSERO_RS12135
         (306 letters)



>FitnessBrowser__HerbieS:HSERO_RS12135
          Length = 306

 Score =  621 bits (1601), Expect = 0.0
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1   VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA 60
           VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA
Sbjct: 1   VATPFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRA 60

Query: 61  VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP 120
           VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP
Sbjct: 61  VLGKYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPTP 120

Query: 121 LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180
           LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE
Sbjct: 121 LYQRPRFGSEAAWQGYAQRLDQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180

Query: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240
           VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF
Sbjct: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240

Query: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG 300
           TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG
Sbjct: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAAIENG 300

Query: 301 SLQEAA 306
           SLQEAA
Sbjct: 301 SLQEAA 306


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: 522
Number of extensions: 11
Number of successful extensions: 1
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
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 HSERO_RS12135 HSERO_RS12135 (xylose isomerase)
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.23486.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-130  420.3   0.0   2.7e-130  420.1   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS12135  HSERO_RS12135 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS12135  HSERO_RS12135 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.1   0.0  2.7e-130  2.7e-130       1     289 [.       6     293 ..       6     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.1 bits;  conditional E-value: 2.7e-130
                                  TIGR04379   1 kvklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgw 68 
                                                +vk+gi+Pi+W+ndDlp+lgg+t+leq+lse ae+g++g+Elgnkfp++p++L+a+l +++le+vsgw
  lcl|FitnessBrowser__HerbieS:HSERO_RS12135   6 NVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRAVLGKYQLECVSGW 73 
                                                59****************************************************************** PP

                                  TIGR04379  69 fsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeeweelaekl 135
                                                +s++l+++sveeei av++hl+ll+a ga+v+v++Ev++siqg   tpl +rp++ +e+ w+ +a++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS12135  74 YSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGA-PTPLYQRPRFgSEAAWQGYAQRL 140
                                                *******************************************9.99********77889******** PP

                                  TIGR04379 136 nklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadR 203
                                                ++++++l ++g++layHhH+g++vet e++d+lm+lt++e vgll+D+GH++fag+dplavl+++ dR
  lcl|FitnessBrowser__HerbieS:HSERO_RS12135 141 DQFARHLLQRGVRLAYHHHMGAYVETPEDLDKLMALTGEE-VGLLFDSGHIAFAGGDPLAVLQRHLDR 207
                                                **************************************99.*************************** PP

                                  TIGR04379 204 iahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPa 271
                                                ++hvH+KDvR++v++ +r++++sFl+av++G+ftvPGdG+idf+++l+ l +++Y+GWlvvEaEqDPa
  lcl|FitnessBrowser__HerbieS:HSERO_RS12135 208 VCHVHCKDVRPAVVKLARNRDWSFLQAVINGAFTVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPA 275
                                                ******************************************************************** PP

                                  TIGR04379 272 kaepleyakkakkyleel 289
                                                +a++++ya++++++l++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS12135 276 VAPSYRYAQMGYRHLSTL 293
                                                ***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (306 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: 11.06
//
[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