Alignments for a candidate for xylB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Escherichia coli BW25113

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate 17625 b3564 xylulokinase (NCBI)

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__Keio:17625
          Length = 484

 Score =  977 bits (2525), Expect = 0.0
 Identities = 484/484 (100%), Positives = 484/484 (100%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60
           MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG
Sbjct: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60

Query: 61  DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG 120
           DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG
Sbjct: 61  DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG 120

Query: 121 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA 180
           NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA
Sbjct: 121 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA 180

Query: 181 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG 240
           KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG
Sbjct: 181 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG 240

Query: 241 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW 300
           VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW
Sbjct: 241 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW 300

Query: 301 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE 360
           AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE
Sbjct: 301 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE 360

Query: 361 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG 420
           LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG
Sbjct: 361 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG 420

Query: 421 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL 480
           DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL
Sbjct: 421 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLL 480

Query: 481 PLMA 484
           PLMA
Sbjct: 481 PLMA 484


Lambda     K      H
   0.319    0.134    0.409 

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: 904
Number of extensions: 21
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: 484
Length of database: 484
Length adjustment: 34
Effective length of query: 450
Effective length of database: 450
Effective search space:   202500
Effective search space used:   202500
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: 52 (24.6 bits)

Align candidate 17625 b3564 (xylulokinase (NCBI))
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

# 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/TIGR01312.hmm
# target sequence database:        /tmp/gapView.29139.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01312  [M=481]
Accession:   TIGR01312
Description: XylB: xylulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     7e-201  653.8   0.0     8e-201  653.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:17625  b3564 xylulokinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17625  b3564 xylulokinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.6   0.0    8e-201    8e-201       1     481 []       3     477 ..       3     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 653.6 bits;  conditional E-value: 8e-201
                       TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmHg 79 
                                     +GiDlgTs+vK++l++e+gev+a ++++ltv++p+p wsEqdpe+w++a+++a+k+l ++++   +++ka++i+GQmHg
  lcl|FitnessBrowser__Keio:17625   3 IGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHS--LQDVKALGIAGQMHG 79 
                                     8***********************************************************88..5************** PP

                       TIGR01312  80 lvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLPkDyl 158
                                     ++lLD++++vlrpaiLWnD r+a+ec+ le++++  +++ +tgnl+++gfTapKllWv++hepe+f++i+kvlLPkDyl
  lcl|FitnessBrowser__Keio:17625  80 ATLLDAQQRVLRPAILWNDGRCAQECTLLEARVP--QSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYL 156
                                     *********************************9..88899************************************** PP

                       TIGR01312 159 rykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkvaaGggdn 237
                                     r+++tge+++++sDA+GT+++dv+kr+ws+ +l+a+dl+++++P+l+e+se++G++ +evak++G+ ++v+v+aGggdn
  lcl|FitnessBrowser__Keio:17625 157 RLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGM-ATVPVVAGGGDN 234
                                     ******************************************************************.99********** PP

                       TIGR01312 238 aagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveel 316
                                     aagA+G+g+v+++++++slGtSGv++av++   s+pe+avhsFchalp++w+ ++v+lsa+s+l+w+++l+g ++v +l
  lcl|FitnessBrowser__Keio:17625 235 AAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPAL 313
                                     ******************************************************************************* PP

                       TIGR01312 317 neeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeir 395
                                      ++a++++++ae+v++lPylsGERtPh++pqa+g+++Glt+++  ++larAvlegv +al+d++d++++ +g+k+++++
  lcl|FitnessBrowser__Keio:17625 314 IAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHA-CGIKPQSVT 391
                                     ********************************************************************9.88******* PP

                       TIGR01312 396 liGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialg.ekdlveecseavvkqkesvepiaenveayeel 472
                                     liGGGa+se+wrq+ladi+g+++++++  + g+alGaA+lA+ia++ ek+l+e++++   +q++   p+a++++ay+ +
  lcl|FitnessBrowser__Keio:17625 392 LIGGGARSEYWRQMLADISGQQLDYRTgGDVGPALGAARLAQIAANpEKSLIELLPQLPLEQSHL--PDAQRYAAYQPR 468
                                     ***************************99*****************9999**********99999..************ PP

                       TIGR01312 473 yerykklye 481
                                      e++++ly+
  lcl|FitnessBrowser__Keio:17625 469 RETFRRLYQ 477
                                     ******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (484 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: 00:00:00.02
# Mc/sec: 8.16
//
[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:

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