GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Paraburkholderia bryophila 376MFSha3.1

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate H281DRAFT_04153 H281DRAFT_04153 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__Burk376:H281DRAFT_04153
          Length = 493

 Score =  503 bits (1294), Expect = e-147
 Identities = 258/487 (52%), Positives = 328/487 (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   MYLGIDLGTSEVKVLLLASNGRVIGTAGSPFTVSRPHQRWAEQNPEDWWAGTQSALAALR 60

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

Query: 119 TGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLD 178
            GNL MPGFTAPKLLWV RHEP+IF +   VLLPKDYLRL++TG   SD SDAAGT+WLD
Sbjct: 121 AGNLAMPGFTAPKLLWVARHEPDIFARTACVLLPKDYLRLQLTGGKVSDPSDAAGTLWLD 180

Query: 179 VAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMAT-VPVVAGGGDNAAG 237
           VAKRDWSD +L AC+++R QMP+L EGS  +G LLPE+A+ +G+A  V V AGGGDNA  
Sbjct: 181 VAKRDWSDSLLAACNMTRAQMPSLAEGSAPSGTLLPELAREYGLADGVIVAAGGGDNATS 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  A+       FLPYLSGERTPHN+P A+GVFFG+ H 
Sbjct: 301 LRWVCKLTS-TDEPTLLAEIEALPAEALTTAPLFLPYLSGERTPHNDPYAQGVFFGMNHA 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+E+   P+ +R+A  + R + +R L
Sbjct: 420 KHGGGETGAALGAARLGWLAAGGDPATV--LSKPPIEKEFTPNPRRHAELRTRLDAYRAL 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: 684
Number of extensions: 31
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 H281DRAFT_04153 H281DRAFT_04153 (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.29094.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.6e-177  575.6   0.0   4.2e-177  575.4   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04153  H281DRAFT_04153 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04153  H281DRAFT_04153 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  575.4   0.0  4.2e-177  4.2e-177       1     480 [.       3     478 ..       3     479 .. 0.98

  Alignments for each domain:
  == domain 1  score: 575.4 bits;  conditional E-value: 4.2e-177
                                    TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekk 66 
                                                  lGiDlgTs+vK+ll+ ++g+vi+++ +++tv++p++ w+Eq+pe+w++ +++al++l++k+  e +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153   3 LGIDLGTSEVKVLLLASNGRVIGTAGSPFTVSRPHQRWAEQNPEDWWAGTQSALAALRAKHPDEFA 68 
                                                  7***************************************************************** PP

                                    TIGR01312  67 eikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTap 132
                                                  +i++i++sGQmHg+vlLD+e++vlrpaiLWnD r+ +ec+el+e+++   l++++gnla++gfTap
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153  69 QIRGIGLSGQMHGAVLLDAEDRVLRPAILWNDMRSDKECAELTERAP--DLHSVAGNLAMPGFTAP 132
                                                  **********************************************9..9**************** PP

                                    TIGR01312 133 KllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldlee 198
                                                  KllWv +hep++far+a vlLPkDylr++Ltg +v++ sDA+GTl++dv+kr+ws++ll+a+++ +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 133 KLLWVARHEPDIFARTACVLLPKDYLRLQLTGGKVSDPSDAAGTLWLDVAKRDWSDSLLAACNMTR 198
                                                  ****************************************************************** PP

                                    TIGR01312 199 sllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvla 264
                                                  +++P+l e+s+ +G++ +e+a+++Gl +gv+vaaGggdna++AiG+g++++g+ +vslGtSGv+ +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 199 AQMPSLAEGSAPSGTLLPELAREYGLADGVIVAAGGGDNATSAIGIGATQPGDGFVSLGTSGVLCV 264
                                                  ****************************************************************** PP

                                    TIGR01312 265 vedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevg..ae 328
                                                  v d+ +++p++avh+Fcha p++w++++v+lsa+s+l w+++l++ +d  +l++e+e+ +++  ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 265 VGDSFRPNPASAVHAFCHAIPDRWHQMSVVLSAASCLRWVCKLTS-TDEPTLLAEIEALPAEalTT 329
                                                  *********************************************.9999*******999883458 PP

                                    TIGR01312 329 gvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikei 394
                                                  + l+lPylsGERtPh+dp a+g+++G++++t ra l +Avlegv++al d+ld+l++ +g++ k +
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 330 APLFLPYLSGERTPHNDPYAQGVFFGMNHATDRALLGYAVLEGVTLALTDGLDALRA-AGTEAKAL 394
                                                  99*******************************************************.67****** PP

                                    TIGR01312 395 rliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesv 459
                                                  +l GGGa+s++w q+lad l+++ +++   e+gaalGaA+l+ +a+g  d + ++s+  ++++ + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 395 SLLGGGARSDYWAQLLADALDTATRKHGgGETGAALGAARLGWLAAGG-DPATVLSKPPIEKEFT- 458
                                                  **************************9989****************96.7999999999998887. PP

                                    TIGR01312 460 epiaenveayeelyerykkly 480
                                                   p+ +++++ +++++ y++ly
  lcl|FitnessBrowser__Burk376:H281DRAFT_04153 459 -PNPRRHAELRTRLDAYRALY 478
                                                  .999**************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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.45
//
[ok]

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

Links

Downloads

Related tools

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:

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:

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:

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:

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