GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucI in Escherichia coli BW25113

Align L-fucose isomerase (EC 5.3.1.25) (characterized)
to candidate 16886 b2802 L-fucose isomerase (NCBI)

Query= BRENDA::P69922
         (591 letters)



>FitnessBrowser__Keio:16886
          Length = 591

 Score = 1211 bits (3132), Expect = 0.0
 Identities = 591/591 (100%), Positives = 591/591 (100%)

Query: 1   MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALLTEKLRHACGAAVECVISDT 60
           MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALLTEKLRHACGAAVECVISDT
Sbjct: 1   MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALLTEKLRHACGAAVECVISDT 60

Query: 61  CIAGMAEAAACEEKFSSQNVGLTITVTPCWCYGSETIDMDPTRPKAIWGFNGTERPGAVY 120
           CIAGMAEAAACEEKFSSQNVGLTITVTPCWCYGSETIDMDPTRPKAIWGFNGTERPGAVY
Sbjct: 61  CIAGMAEAAACEEKFSSQNVGLTITVTPCWCYGSETIDMDPTRPKAIWGFNGTERPGAVY 120

Query: 121 LAAALAAHSQKGIPAFSIYGHDVQDADDTSIPADVEEKLLRFARAGLAVASMKGKSYLSL 180
           LAAALAAHSQKGIPAFSIYGHDVQDADDTSIPADVEEKLLRFARAGLAVASMKGKSYLSL
Sbjct: 121 LAAALAAHSQKGIPAFSIYGHDVQDADDTSIPADVEEKLLRFARAGLAVASMKGKSYLSL 180

Query: 181 GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDEAELEMALAWADKNFRY 240
           GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDEAELEMALAWADKNFRY
Sbjct: 181 GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDEAELEMALAWADKNFRY 240

Query: 241 GEDENNKQYQRNAEQSRAVLRESLLMAMCIRDMMQGNSKLADIGRVEESLGYNAIAAGFQ 300
           GEDENNKQYQRNAEQSRAVLRESLLMAMCIRDMMQGNSKLADIGRVEESLGYNAIAAGFQ
Sbjct: 241 GEDENNKQYQRNAEQSRAVLRESLLMAMCIRDMMQGNSKLADIGRVEESLGYNAIAAGFQ 300

Query: 301 GQRHWTDQYPNGDTAEAILNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA 360
           GQRHWTDQYPNGDTAEAILNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA
Sbjct: 301 GQRHWTDQYPNGDTAEAILNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA 360

Query: 361 DVRTYWSPEAIERVTGHKLDGLAEHGIIHLINSGSAALDGSCKQRDSEGNPTMKPHWEIS 420
           DVRTYWSPEAIERVTGHKLDGLAEHGIIHLINSGSAALDGSCKQRDSEGNPTMKPHWEIS
Sbjct: 361 DVRTYWSPEAIERVTGHKLDGLAEHGIIHLINSGSAALDGSCKQRDSEGNPTMKPHWEIS 420

Query: 421 QQEADACLAATEWCPAIHEYFRGGGYSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS 480
           QQEADACLAATEWCPAIHEYFRGGGYSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS
Sbjct: 421 QQEADACLAATEWCPAIHEYFRGGGYSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS 480

Query: 481 VELPKDVHDILNKRTNSTWPTTWFAPRLTGKGPFTDVYSVMANWGANHGVLTIGHVGADF 540
           VELPKDVHDILNKRTNSTWPTTWFAPRLTGKGPFTDVYSVMANWGANHGVLTIGHVGADF
Sbjct: 481 VELPKDVHDILNKRTNSTWPTTWFAPRLTGKGPFTDVYSVMANWGANHGVLTIGHVGADF 540

Query: 541 ITLASMLRIPVCMHNVEETKVYRPSAWAAHGMDIEGQDYRACQNYGPLYKR 591
           ITLASMLRIPVCMHNVEETKVYRPSAWAAHGMDIEGQDYRACQNYGPLYKR
Sbjct: 541 ITLASMLRIPVCMHNVEETKVYRPSAWAAHGMDIEGQDYRACQNYGPLYKR 591


Lambda     K      H
   0.318    0.133    0.410 

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: 1304
Number of extensions: 25
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: 591
Length of database: 591
Length adjustment: 37
Effective length of query: 554
Effective length of database: 554
Effective search space:   306916
Effective search space used:   306916
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: 53 (25.0 bits)

Align candidate 16886 b2802 (L-fucose isomerase (NCBI))
to HMM TIGR01089 (fucI: L-fucose isomerase (EC 5.3.1.25))

# 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/TIGR01089.hmm
# target sequence database:        /tmp/gapView.3913510.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01089  [M=587]
Accession:   TIGR01089
Description: fucI: L-fucose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1252.7   1.3          0 1252.5   1.3    1.0  1  lcl|FitnessBrowser__Keio:16886  b2802 L-fucose isomerase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16886  b2802 L-fucose isomerase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1252.5   1.3         0         0       2     587 .]       5     590 ..       4     590 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1252.5 bits;  conditional E-value: 0
                       TIGR01089   2 klpkigirptidgrrmgvresleektlnlakavaellseklrhadgaavecviadstiggvaeaaacaekferenvglt 80 
                                     +lpkigirp+idgrrmgvreslee+t+n+aka+a+ll+eklrha+gaavecvi+d++i+g+aeaaac+ekf+++nvglt
  lcl|FitnessBrowser__Keio:16886   5 SLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALLTEKLRHACGAAVECVISDTCIAGMAEAAACEEKFSSQNVGLT 83 
                                     79***************************************************************************** PP

                       TIGR01089  81 itvtscwcygsetidmdphrpkaiwgfngterpgavylaaalaghsqkglpafsiygrdvqdaddtsipedveekllrf 159
                                     itvt+cwcygsetidmdp+rpkaiwgfngterpgavylaaala+hsqkg+pafsiyg+dvqdaddtsip+dveekllrf
  lcl|FitnessBrowser__Keio:16886  84 ITVTPCWCYGSETIDMDPTRPKAIWGFNGTERPGAVYLAAALAAHSQKGIPAFSIYGHDVQDADDTSIPADVEEKLLRF 162
                                     ******************************************************************************* PP

                       TIGR01089 160 araglavaslrgksylslgsvsmgiagsivnkdffqeylgmrneavdlteikrrldekiydeeelelalawvekyckvg 238
                                     araglavas++gksylslg+vsmgiagsiv+++ff+++lgm+++avd+te++rr+d+kiyde+ele+alaw++k++++g
  lcl|FitnessBrowser__Keio:16886 163 ARAGLAVASMKGKSYLSLGGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDEAELEMALAWADKNFRYG 241
                                     ******************************************************************************* PP

                       TIGR01089 239 edenskekqrnaeqkaavleevvkmaiiirdlmvgnpklaelgfaeealgynaiaagfqgqrhwtdqypngdfaealln 317
                                     eden+k++qrnaeq++avl+e+++ma++ird+m+gn+kla++g++ee+lgynaiaagfqgqrhwtdqypngd+aea+ln
  lcl|FitnessBrowser__Keio:16886 242 EDENNKQYQRNAEQSRAVLRESLLMAMCIRDMMQGNSKLADIGRVEESLGYNAIAAGFQGQRHWTDQYPNGDTAEAILN 320
                                     ******************************************************************************* PP

                       TIGR01089 318 ssfdwngvreafvvatendslngvamllghqltgkaqifadvrtywspeavervtgkkleglaengiihlinsgsaald 396
                                     ssfdwngvre+fvvatendslngvaml+ghqltg+aq+fadvrtywspea+ervtg+kl+glae+giihlinsgsaald
  lcl|FitnessBrowser__Keio:16886 321 SSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFADVRTYWSPEAIERVTGHKLDGLAEHGIIHLINSGSAALD 399
                                     ******************************************************************************* PP

                       TIGR01089 397 gsgksrdaegnptlkeawelteeeaeaclkatewcpavreyfrggglssrfltkggvpvtltrvnlikglgpvlqiaeg 475
                                     gs+k+rd+egnpt+k++we++++ea+acl+atewcpa++eyfrggg+ssrflt+ggvp+t+trvn+ikglgpvlqiaeg
  lcl|FitnessBrowser__Keio:16886 400 GSCKQRDSEGNPTMKPHWEISQQEADACLAATEWCPAIHEYFRGGGYSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEG 478
                                     ******************************************************************************* PP

                       TIGR01089 476 wsveldkdvhdklnkrtnetwpttwfvprltgkgaftdvysvmanwganhgvltyghvgadlitlasmlripvcmhnve 554
                                     wsvel+kdvhd+lnkrtn+twpttwf+prltgkg+ftdvysvmanwganhgvlt+ghvgad+itlasmlripvcmhnve
  lcl|FitnessBrowser__Keio:16886 479 WSVELPKDVHDILNKRTNSTWPTTWFAPRLTGKGPFTDVYSVMANWGANHGVLTIGHVGADFITLASMLRIPVCMHNVE 557
                                     ******************************************************************************* PP

                       TIGR01089 555 ekeifrpsawnafgmdkegqdyracqnygplyk 587
                                     e++++rpsaw+a+gmd+egqdyracqnygplyk
  lcl|FitnessBrowser__Keio:16886 558 ETKVYRPSAWAAHGMDIEGQDYRACQNYGPLYK 590
                                     ********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (587 nodes)
Target sequences:                          1  (591 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: 25.73
//
[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