Alignments for a candidate for xylB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Burkholderia phytofirmans PsJN

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate BPHYT_RS16080 BPHYT_RS16080 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__BFirm:BPHYT_RS16080
          Length = 493

 Score =  509 bits (1311), Expect = e-149
 Identities = 264/487 (54%), Positives = 329/487 (67%), Gaps = 8/487 (1%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60
           MY+GIDLGTS VKV+LL   G V+       TVSRPH  W+EQ+PE WW  T  A+ AL 
Sbjct: 1   MYLGIDLGTSEVKVLLLASDGRVIGTAGSPFTVSRPHQRWAEQNPEDWWAGTRTALAALR 60

Query: 61  DQH--SLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVI 118
            +H      ++ +G++GQMHGA LLDAQ RVLRPAILWND R  +EC  L  R P+   +
Sbjct: 61  AKHPDEFAQIRGIGLSGQMHGAVLLDAQDRVLRPAILWNDMRSDKECAELTERAPELHSV 120

Query: 119 TGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLD 178
            GNL MPGFTAPKLLWV RHEPEIF Q   VLLPKDYLRL++TG   SD SDAAGT+WLD
Sbjct: 121 AGNLAMPGFTAPKLLWVARHEPEIFAQTACVLLPKDYLRLQLTGGKVSDPSDAAGTLWLD 180

Query: 179 VAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMAT-VPVVAGGGDNAAG 237
           VAKRDWSD +L AC++SR QMP+L EGSE +G LLP VA+ +G++  V V AGGGDNA  
Sbjct: 181 VAKRDWSDSLLAACNMSRAQMPSLAEGSEPSGTLLPSVAREFGLSDGVIVAAGGGDNATS 240

Query: 238 AVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASC 297
           A+G+G        +SLGTSGV   V + F   P SAVH+FCHA+P RWH MSV+LSAASC
Sbjct: 241 AIGIGATQPGDGFVSLGTSGVLCVVGDSFRPNPASAVHAFCHAIPDRWHQMSVVLSAASC 300

Query: 298 LDWAAKLTGLSNVPALIA--AAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQ 355
           L W  KLT  ++ P L+A   A  AD       FLPYLSGERTPHN+P A+GVFFG+TH 
Sbjct: 301 LRWVCKLTS-TDEPTLLAEIEALPADALNTAPLFLPYLSGERTPHNDPYAQGVFFGMTHA 359

Query: 356 HGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLD 415
                L  AVLEGV  AL DG+D + A G + ++++L+GGGARS+YW Q+LAD       
Sbjct: 360 TDRALLGYAVLEGVTLALTDGLDALRAAGTEAKALSLLGGGARSDYWAQLLADALDTATR 419

Query: 416 YRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRL 475
              GG+ G ALGAARL  +AA  + + +  L + P+ +   P+ +R+A  + R E +R L
Sbjct: 420 KHGGGETGAALGAARLGWLAAGGDPATV--LTKPPIAKEFTPNPRRHAELRARLEAYRAL 477

Query: 476 YQQLLPL 482
           Y+ + PL
Sbjct: 478 YRHVRPL 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: 708
Number of extensions: 35
Number of successful extensions: 5
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: 493
Length adjustment: 34
Effective length of query: 450
Effective length of database: 459
Effective search space:   206550
Effective search space used:   206550
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 BPHYT_RS16080 BPHYT_RS16080 (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.23767.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     3e-177  575.9   0.0   3.5e-177  575.7   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16080  BPHYT_RS16080 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16080  BPHYT_RS16080 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.7   0.0  3.5e-177  3.5e-177       1     480 [.       3     478 ..       3     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 575.7 bits;  conditional E-value: 3.5e-177
                                TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeika 70 
                                              lGiDlgTs+vK+ll+ + g+vi+++ +++tv++p++ w+Eq+pe+w++ + +al++l++k+  e ++i++
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080   3 LGIDLGTSEVKVLLLASDGRVIGTAGSPFTVSRPHQRWAEQNPEDWWAGTRTALAALRAKHPDEFAQIRG 72 
                                              7********************************************************************* PP

                                TIGR01312  71 isisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkh 140
                                              i++sGQmHg+vlLD++++vlrpaiLWnD r+ +ec+el+e+++  el++++gnla++gfTapKllWv +h
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080  73 IGLSGQMHGAVLLDAQDRVLRPAILWNDMRSDKECAELTERAP--ELHSVAGNLAMPGFTAPKLLWVARH 140
                                              ******************************************9..9************************ PP

                                TIGR01312 141 epevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessek 210
                                              epe+fa++a vlLPkDylr++Ltg +v++ sDA+GTl++dv+kr+ws++ll+a++++++++P+l e+se 
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080 141 EPEIFAQTACVLLPKDYLRLQLTGGKVSDPSDAAGTLWLDVAKRDWSDSLLAACNMSRAQMPSLAEGSEP 210
                                              ********************************************************************** PP

                                TIGR01312 211 aGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsF 280
                                              +G++ ++va+++Gl++gv+vaaGggdna++AiG+g++++g+ +vslGtSGv+ +v d+ +++p++avh+F
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080 211 SGTLLPSVAREFGLSDGVIVAAGGGDNATSAIGIGATQPGDGFVSLGTSGVLCVVGDSFRPNPASAVHAF 280
                                              ********************************************************************** PP

                                TIGR01312 281 chalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevga..egvlllPylsGERtPhldpqa 348
                                              cha p++w++++v+lsa+s+l w+++l++ +d  +l++e+e+ +++a  ++ l+lPylsGERtPh+dp a
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080 281 CHAIPDRWHQMSVVLSAASCLRWVCKLTS-TDEPTLLAEIEALPADAlnTAPLFLPYLSGERTPHNDPYA 349
                                              *****************************.9999*********999644789****************** PP

                                TIGR01312 349 rgsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglev 418
                                              +g+++G+t++t ra l +Avlegv++al d+ld+l++ +g++ k ++l GGGa+s++w q+lad l+++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080 350 QGVFFGMTHATDRALLGYAVLEGVTLALTDGLDALRA-AGTEAKALSLLGGGARSDYWAQLLADALDTAT 418
                                              *************************************.67****************************** PP

                                TIGR01312 419 vvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                              +++   e+gaalGaA+l+ +a+g  d + ++++  ++++ +  p+ +++++ + ++e y++ly
  lcl|FitnessBrowser__BFirm:BPHYT_RS16080 419 RKHGgGETGAALGAARLGWLAAGG-DPATVLTKPPIAKEFT--PNPRRHAELRARLEAYRALY 478
                                              **9989****************96.7999999999988877..9999*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (493 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: 7.09
//
[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