Alignments for a candidate for fucI in Escherichia coli BW25113

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.29968.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.50
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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