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

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.10162.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.02
//
[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