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_RS19340 BWI76_RS19340 xylulokinase

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



>FitnessBrowser__Koxy:BWI76_RS19340
          Length = 487

 Score =  508 bits (1309), Expect = e-148
 Identities = 253/446 (56%), Positives = 314/446 (70%), Gaps = 6/446 (1%)

Query: 1   MYIGIDLGTSGVKAILLNEQGEVVASHTEKLNVSRPHPLWSEQDPEHWWLATDSAMKALG 60
           MY+GIDLGTS VKA++++E  EV+ASH+  L++ RPHP WSEQ P+ WW AT+  M  L 
Sbjct: 1   MYLGIDLGTSEVKALVIDENNEVIASHSAPLSIQRPHPHWSEQSPQSWWEATEYLMATLR 60

Query: 61  ---AQHSLRAVKALGIAGQMHGATLLDKQQRVLRPAILWNDGRCGEECALLEEKVSRSRQ 117
              AQH   A+KA+G++GQMHGA LLD +  V+RPAILWND RC  ECA LEE      Q
Sbjct: 61  EKCAQH-WPAIKAIGLSGQMHGAVLLDAEGEVIRPAILWNDTRCAAECAELEEMAPELHQ 119

Query: 118 ITGNLMMPGFTAPKLLWVQRHEPEIFRQVDKVLLPKDYLRLRMTGEFASDMSDAAGTMWM 177
           + GNL MPGFTAPKLLWV+RHEP+ F++   VLLPKDYLR RMTG+  SDMSDAAGT+W+
Sbjct: 120 VAGNLAMPGFTAPKLLWVRRHEPQYFQRTATVLLPKDYLRYRMTGKKVSDMSDAAGTLWL 179

Query: 178 DVARRDWSDEMLAACGLSRDNMPALFEGCEVTGSLRPAVAQAWNM-PEVLVVAGGGDNAA 236
           DVA+RDWSD +L  CGLSR  MP L EGCEV+ +L P VA+ W +   V V  GGGDNA 
Sbjct: 180 DVAKRDWSDSLLDKCGLSRSQMPTLVEGCEVSATLDPQVAERWGLNASVAVAGGGGDNAV 239

Query: 237 GAVGVGMADAGQAMLSLGTSGVYFAVSDGFLSKPESAVHSFCHALPGRWHLMSVMLSAAS 296
            A+GVG    G A +SLGTSGV F V+D +   P+SAVH+FCH LP  WH MSVMLSAAS
Sbjct: 240 SAIGVGAVSPGDAFISLGTSGVLFVVTDAYRPAPQSAVHAFCHVLPNLWHQMSVMLSAAS 299

Query: 297 CLDWAATLTGLGTVPALIAAAEAANDD-ADPVWFLPYLSGERTPHNNPQAKGVFFGLTHQ 355
           CL W   LTG   V  L   A+ + ++ A   +FLPYLSGERTPHN+P A+G+F+G+TH 
Sbjct: 300 CLQWFCRLTGTTEVALLEEIAQLSEEEKAHAPFFLPYLSGERTPHNDPDARGMFWGMTHS 359

Query: 356 HGPAELARAVLEGVGYALADGMDVVHACGVKPESVTLIGGGARSAYWRQMLADISGQQLD 415
              A+L  AVLEGV + + DG+ V+   G + E  +L+GGGARS +W Q+LADI    + 
Sbjct: 360 SLRAQLGYAVLEGVSFGINDGLRVLKESGTRIEQCSLVGGGARSPFWAQLLADILDMPVV 419

Query: 416 FRTGGDVGPALGAARLAQLALHRNVA 441
              GG+ G ALGAARLA LA  + +A
Sbjct: 420 THKGGETGGALGAARLACLAAGKPLA 445


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: 760
Number of extensions: 29
Number of successful extensions: 4
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: 487
Length adjustment: 34
Effective length of query: 450
Effective length of database: 453
Effective search space:   203850
Effective search space used:   203850
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_RS19340 BWI76_RS19340 (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.26979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-201  656.2   0.0   1.6e-201  656.0   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS19340  BWI76_RS19340 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS19340  BWI76_RS19340 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  656.0   0.0  1.6e-201  1.6e-201       1     480 [.       3     478 ..       3     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 656.0 bits;  conditional E-value: 1.6e-201
                               TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikai 71 
                                             lGiDlgTs+vKal++de++evias+sa+l++++p+p+wsEq p++w+ea+e ++++l+ek+++++ +ikai
  lcl|FitnessBrowser__Koxy:BWI76_RS19340   3 LGIDLGTSEVKALVIDENNEVIASHSAPLSIQRPHPHWSEQSPQSWWEATEYLMATLREKCAQHWPAIKAI 73 
                                             7********************************************************************** PP

                               TIGR01312  72 sisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhep 142
                                             ++sGQmHg+vlLD+eg+v+rpaiLWnDtr+a+ec+elee+++  el++++gnla++gfTapKllWvr+hep
  lcl|FitnessBrowser__Koxy:BWI76_RS19340  74 GLSGQMHGAVLLDAEGEVIRPAILWNDTRCAAECAELEEMAP--ELHQVAGNLAMPGFTAPKLLWVRRHEP 142
                                             *****************************************9..9************************** PP

                               TIGR01312 143 evfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGk 213
                                             + f+r+a+vlLPkDylry++tg++v+++sDA+GTl++dv+kr+ws++ll+++ l++s++P+lve++e++++
  lcl|FitnessBrowser__Koxy:BWI76_RS19340 143 QYFQRTATVLLPKDYLRYRMTGKKVSDMSDAAGTLWLDVAKRDWSDSLLDKCGLSRSQMPTLVEGCEVSAT 213
                                             *********************************************************************** PP

                               TIGR01312 214 vreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchal 284
                                             ++++va+++Gl+++v va+Gggdna++AiG+g+v++g++++slGtSGv+++v+d++++ p++avh+Fch+l
  lcl|FitnessBrowser__Koxy:BWI76_RS19340 214 LDPQVAERWGLNASVAVAGGGGDNAVSAIGVGAVSPGDAFISLGTSGVLFVVTDAYRPAPQSAVHAFCHVL 284
                                             *********************************************************************** PP

                               TIGR01312 285 pgkwyplgvtlsatsalewlkellgeldveelneeaekvevg.aegvlllPylsGERtPhldpqargsliG 354
                                             p+ w++++v+lsa+s+l+w+++l+g+++v+ l+e a+ +e++ a++ ++lPylsGERtPh+dp+arg+++G
  lcl|FitnessBrowser__Koxy:BWI76_RS19340 285 PNLWHQMSVMLSAASCLQWFCRLTGTTEVALLEEIAQLSEEEkAHAPFFLPYLSGERTPHNDPDARGMFWG 355
                                             *****************************99999999887666**************************** PP

                               TIGR01312 355 ltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.ee 424
                                             +t+++ ra+l +Avlegv+f+++d+l +lke +g++i++++l+GGGa+s++w q+ladil+++vv+++  e
  lcl|FitnessBrowser__Koxy:BWI76_RS19340 356 MTHSSLRAQLGYAVLEGVSFGINDGLRVLKE-SGTRIEQCSLVGGGARSPFWAQLLADILDMPVVTHKgGE 425
                                             *******************************.88**********************************99* PP

                               TIGR01312 425 egaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                             +g alGaA+lA++a+g+  l+++c++  v+q+++++p+ ++  + +++y+++++ly
  lcl|FitnessBrowser__Koxy:BWI76_RS19340 426 TGGALGAARLACLAAGK-PLAAVCEKPEVWQTWRADPVRHQ--TLMRRYAQFNALY 478
                                             ***************96.8***************7777655..5888899998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (487 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: 11.44
//
[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