Alignments for a candidate for xylB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Klebsiella michiganensis M5al

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate BWI76_RS27020 BWI76_RS27020 xylulokinase

Query= reanno::Koxy:BWI76_RS27020
         (484 letters)



>FitnessBrowser__Koxy:BWI76_RS27020
          Length = 484

 Score =  981 bits (2537), Expect = 0.0
 Identities = 484/484 (100%), Positives = 484/484 (100%)

Query: 1   MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG 60
           MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG
Sbjct: 1   MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG 60

Query: 61  AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG 120
           AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG
Sbjct: 61  AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQITG 120

Query: 121 NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA 180
           NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA
Sbjct: 121 NLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVA 180

Query: 181 RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG 240
           RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG
Sbjct: 181 RRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNMPEVLVVAGGGDNAAGAVG 240

Query: 241 VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW 300
           VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW
Sbjct: 241 VGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAASCLDW 300

Query: 301 AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE 360
           AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE
Sbjct: 301 AATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPAE 360

Query: 361 LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG 420
           LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG
Sbjct: 361 LARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTGG 420

Query: 421 DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL 480
           DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL
Sbjct: 421 DVGPALGAARLAQLALHRNVAFSDLLPQLPLEQAHLPDAERFARYAPRRETFRQIYQQLL 480

Query: 481 PLMS 484
           PLMS
Sbjct: 481 PLMS 484


Lambda     K      H
   0.320    0.134    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: 944
Number of extensions: 32
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 BWI76_RS27020 BWI76_RS27020 (xylulokinase)
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.16180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.2e-191  621.0   0.0   7.1e-191  620.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS27020  BWI76_RS27020 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS27020  BWI76_RS27020 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.8   0.0  7.1e-191  7.1e-191       1     481 []       3     477 ..       3     477 .. 0.98

  Alignments for each domain:
  == domain 1  score: 620.8 bits;  conditional E-value: 7.1e-191
                               TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikai 71 
                                             +GiDlgTs+vKa+l++e+gev+as++++l+v++p+p wsEqdpe+w+ a+++a+k+l ++++   +++ka+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020   3 IGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALGAQHS--LRAVKAL 71 
                                             8***********************************************************88..59***** PP

                               TIGR01312  72 sisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhep 142
                                             +i+GQmHg++lLD++++vlrpaiLWnD r+ eec+ lee++   +++++tgnl+++gfTapKllWv++hep
  lcl|FitnessBrowser__Koxy:BWI76_RS27020  72 GIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVS--RSRQITGNLMMPGFTAPKLLWVQRHEP 140
                                             *****************************************7..9************************** PP

                               TIGR01312 143 evfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGk 213
                                             e+f++++kvlLPkDylr+++tge+++++sDA+GT++ dv++r+ws+e+l+a+ l+++ +P+l+e++e++G+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 141 EIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWMDVARRDWSDEMLAACGLSRDNMPALFEGCEVTGS 211
                                             *********************************************************************** PP

                               TIGR01312 214 vreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchal 284
                                             +r++va+++ +  +v v+aGggdnaagA+G+g+ ++g++++slGtSGv++av+d   s+pe+avhsFchal
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 212 LRPAVAQAWNM-PEVLVVAGGGDNAAGAVGVGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHAL 281
                                             *********99.78********************************************************* PP

                               TIGR01312 285 pgkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGl 355
                                             pg+w+ ++v+lsa+s+l+w++ l+g  +v +l ++ae+++ +a++v++lPylsGERtPh++pqa+g+++Gl
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 282 PGRWHLMSVMLSAASCLDWAATLTGLGTVPALIAAAEAANDDADPVWFLPYLSGERTPHNNPQAKGVFFGL 352
                                             *********************************************************************** PP

                               TIGR01312 356 tanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eee 425
                                             t+++  a+larAvlegv +al+d++d++++ +g+k+++++liGGGa+s++wrq+ladi+g++++ ++  + 
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 353 THQHGPAELARAVLEGVGYALADGMDVVHA-CGVKPESVTLIGGGARSAYWRQMLADISGQQLDFRTgGDV 422
                                             *****************************9.88**********************************99** PP

                               TIGR01312 426 gaalGaAilAaialg.ekdlveecseavvkqkesvepiaenveayeelyerykklye 481
                                             g+alGaA+lA++al+ + +  +++++   +q +   p+ae+ ++y+ + e+++++y+
  lcl|FitnessBrowser__Koxy:BWI76_RS27020 423 GPALGAARLAQLALHrNVAFSDLLPQLPLEQAHL--PDAERFARYAPRRETFRQIYQ 477
                                             **************96666677788888887777..******************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.58
//
[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