Alignments for a candidate for fucI in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for fucI in Klebsiella michiganensis M5al

Align L-fucose isomerase (EC 5.3.1.25) (characterized)
to candidate BWI76_RS22925 BWI76_RS22925 L-fucose isomerase

Query= BRENDA::P69922
         (591 letters)



>FitnessBrowser__Koxy:BWI76_RS22925
          Length = 591

 Score = 1141 bits (2952), Expect = 0.0
 Identities = 549/591 (92%), Positives = 575/591 (97%)

Query: 1   MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALLTEKLRHACGAAVECVISDT 60
           MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAAL+ EKLRHACGA +ECVI+D+
Sbjct: 1   MKKISLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALIAEKLRHACGAQIECVIADS 60

Query: 61  CIAGMAEAAACEEKFSSQNVGLTITVTPCWCYGSETIDMDPTRPKAIWGFNGTERPGAVY 120
           CIAGMAE+AACEEKFSSQNVG+TITVTPCWCYGSETIDMDP RPKAIWGFNGTERPGAVY
Sbjct: 61  CIAGMAESAACEEKFSSQNVGVTITVTPCWCYGSETIDMDPLRPKAIWGFNGTERPGAVY 120

Query: 121 LAAALAAHSQKGIPAFSIYGHDVQDADDTSIPADVEEKLLRFARAGLAVASMKGKSYLSL 180
           LAAALAAHSQKGIPAFSIYGHDVQDADDT+IP DVEEKLLRFARAGLAVASMKGKSYLS+
Sbjct: 121 LAAALAAHSQKGIPAFSIYGHDVQDADDTTIPPDVEEKLLRFARAGLAVASMKGKSYLSV 180

Query: 181 GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDEAELEMALAWADKNFRY 240
           GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDE+ELEMALAWADKNFRY
Sbjct: 181 GGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRIDQKIYDESELEMALAWADKNFRY 240

Query: 241 GEDENNKQYQRNAEQSRAVLRESLLMAMCIRDMMQGNSKLADIGRVEESLGYNAIAAGFQ 300
           GED+N +QY+RNAEQSRAVL+ESLLMAMCIRDMMQGNSKLA+ G VEESLGYNAIAAGFQ
Sbjct: 241 GEDQNAQQYKRNAEQSRAVLKESLLMAMCIRDMMQGNSKLAEKGLVEESLGYNAIAAGFQ 300

Query: 301 GQRHWTDQYPNGDTAEAILNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA 360
           GQRHWTDQYPNGDTAEA+LNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA
Sbjct: 301 GQRHWTDQYPNGDTAEALLNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVFA 360

Query: 361 DVRTYWSPEAIERVTGHKLDGLAEHGIIHLINSGSAALDGSCKQRDSEGNPTMKPHWEIS 420
           DVRTYWSPEA+ERVTG  L GLAEHGIIHLINSGSAALDG+CKQRD++G PTMKPHWEIS
Sbjct: 361 DVRTYWSPEAVERVTGQPLTGLAEHGIIHLINSGSAALDGACKQRDADGKPTMKPHWEIS 420

Query: 421 QQEADACLAATEWCPAIHEYFRGGGYSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS 480
           QQEADACLAATEWCPAIHEYFRGGG+SSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS
Sbjct: 421 QQEADACLAATEWCPAIHEYFRGGGFSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWS 480

Query: 481 VELPKDVHDILNKRTNSTWPTTWFAPRLTGKGPFTDVYSVMANWGANHGVLTIGHVGADF 540
           VELPK +HD L+ RTNSTWPTTWFAPRLTGKGPF+DVYSVMANWGANHGVLTIGHVGADF
Sbjct: 481 VELPKAMHDQLDARTNSTWPTTWFAPRLTGKGPFSDVYSVMANWGANHGVLTIGHVGADF 540

Query: 541 ITLASMLRIPVCMHNVEETKVYRPSAWAAHGMDIEGQDYRACQNYGPLYKR 591
           ITLASMLRIPVCMHNVEE K+YRPS+W+AHGMD EGQDYRACQNYGPLYKR
Sbjct: 541 ITLASMLRIPVCMHNVEEAKIYRPSSWSAHGMDSEGQDYRACQNYGPLYKR 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: 1274
Number of extensions: 29
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 BWI76_RS22925 BWI76_RS22925 (L-fucose isomerase)
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.17469.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 1214.6   0.6          0 1214.4   0.6    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22925  BWI76_RS22925 L-fucose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22925  BWI76_RS22925 L-fucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1214.4   0.6         0         0       2     587 .]       5     590 ..       4     590 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1214.4 bits;  conditional E-value: 0
                               TIGR01089   2 klpkigirptidgrrmgvresleektlnlakavaellseklrhadgaavecviadstiggvaeaaacaekf 72 
                                             +lpkigirp+idgrrmgvreslee+t+n+aka+a+l++eklrha+ga++ecviads+i+g+ae+aac+ekf
  lcl|FitnessBrowser__Koxy:BWI76_RS22925   5 SLPKIGIRPVIDGRRMGVRESLEEQTMNMAKATAALIAEKLRHACGAQIECVIADSCIAGMAESAACEEKF 75 
                                             79********************************************************************* PP

                               TIGR01089  73 erenvgltitvtscwcygsetidmdphrpkaiwgfngterpgavylaaalaghsqkglpafsiygrdvqda 143
                                             +++nvg+titvt+cwcygsetidmdp rpkaiwgfngterpgavylaaala+hsqkg+pafsiyg+dvqda
  lcl|FitnessBrowser__Koxy:BWI76_RS22925  76 SSQNVGVTITVTPCWCYGSETIDMDPLRPKAIWGFNGTERPGAVYLAAALAAHSQKGIPAFSIYGHDVQDA 146
                                             *********************************************************************** PP

                               TIGR01089 144 ddtsipedveekllrfaraglavaslrgksylslgsvsmgiagsivnkdffqeylgmrneavdlteikrrl 214
                                             ddt+ip dveekllrfaraglavas++gksyls+g+vsmgiagsiv+++ff+++lgm+++avd+te++rr+
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 147 DDTTIPPDVEEKLLRFARAGLAVASMKGKSYLSVGGVSMGIAGSIVDHNFFESWLGMKVQAVDMTELRRRI 217
                                             *********************************************************************** PP

                               TIGR01089 215 dekiydeeelelalawvekyckvgedenskekqrnaeqkaavleevvkmaiiirdlmvgnpklaelgfaee 285
                                             d+kiyde ele+alaw++k++++ged+n ++++rnaeq++avl+e+++ma++ird+m+gn+klae g +ee
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 218 DQKIYDESELEMALAWADKNFRYGEDQNAQQYKRNAEQSRAVLKESLLMAMCIRDMMQGNSKLAEKGLVEE 288
                                             *********************************************************************** PP

                               TIGR01089 286 algynaiaagfqgqrhwtdqypngdfaeallnssfdwngvreafvvatendslngvamllghqltgkaqif 356
                                             +lgynaiaagfqgqrhwtdqypngd+aeallnssfdwngvre+fvvatendslngvaml+ghqltg+aq+f
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 289 SLGYNAIAAGFQGQRHWTDQYPNGDTAEALLNSSFDWNGVREPFVVATENDSLNGVAMLMGHQLTGTAQVF 359
                                             *********************************************************************** PP

                               TIGR01089 357 advrtywspeavervtgkkleglaengiihlinsgsaaldgsgksrdaegnptlkeawelteeeaeaclka 427
                                             advrtywspeavervtg+ l+glae+giihlinsgsaaldg++k+rda+g+pt+k++we++++ea+acl+a
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 360 ADVRTYWSPEAVERVTGQPLTGLAEHGIIHLINSGSAALDGACKQRDADGKPTMKPHWEISQQEADACLAA 430
                                             *********************************************************************** PP

                               TIGR01089 428 tewcpavreyfrggglssrfltkggvpvtltrvnlikglgpvlqiaegwsveldkdvhdklnkrtnetwpt 498
                                             tewcpa++eyfrggg+ssrflt+ggvp+t+trvn+ikglgpvlqiaegwsvel+k +hd+l+ rtn+twpt
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 431 TEWCPAIHEYFRGGGFSSRFLTEGGVPFTMTRVNIIKGLGPVLQIAEGWSVELPKAMHDQLDARTNSTWPT 501
                                             *********************************************************************** PP

                               TIGR01089 499 twfvprltgkgaftdvysvmanwganhgvltyghvgadlitlasmlripvcmhnveekeifrpsawnafgm 569
                                             twf+prltgkg+f dvysvmanwganhgvlt+ghvgad+itlasmlripvcmhnvee +i+rps+w+a+gm
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 502 TWFAPRLTGKGPFSDVYSVMANWGANHGVLTIGHVGADFITLASMLRIPVCMHNVEEAKIYRPSSWSAHGM 572
                                             *********************************************************************** PP

                               TIGR01089 570 dkegqdyracqnygplyk 587
                                             d egqdyracqnygplyk
  lcl|FitnessBrowser__Koxy:BWI76_RS22925 573 DSEGQDYRACQNYGPLYK 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 8.82
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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