Alignments for a candidate for xylB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Dyella japonica UNC79MFTsu3.2

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate N515DRAFT_3230 N515DRAFT_3230 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3230
          Length = 490

 Score =  561 bits (1445), Expect = e-164
 Identities = 290/491 (59%), Positives = 348/491 (70%), Gaps = 11/491 (2%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKAL- 59
           M++G+DLGTS VK +L++  G V A  ++ LTVS P P WSEQDP  WW+A   A+  L 
Sbjct: 1   MFLGLDLGTSAVKAVLVDAAGAVRAVASQPLTVSHPRPRWSEQDPVDWWRAAVAAIDELL 60

Query: 60  ----GDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQS 115
                D      V A+G++GQMHGATLLD   RVLRPAILWNDGR   +C  +E  +P  
Sbjct: 61  QAAARDGIPASRVAAIGLSGQMHGATLLDRSDRVLRPAILWNDGRSDAQCRWMET-LPDF 119

Query: 116 RVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTM 175
             ITGNL MPGFTAPKL WV+ HEP +F  + KVLLPKDYLRL +TG++ASD+SDAAGT+
Sbjct: 120 HAITGNLAMPGFTAPKLAWVREHEPSVFDAVAKVLLPKDYLRLCLTGDYASDVSDAAGTL 179

Query: 176 WLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNA 235
           WLDV KR WSD ML AC LSR+QMP ++EGSE  G L  E+A+ WGMA VPV AGGGDNA
Sbjct: 180 WLDVGKRQWSDPMLAACGLSREQMPGVHEGSESAGRLRAELAERWGMARVPVAAGGGDNA 239

Query: 236 AGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAA 295
           AGAVG G+V   QAMLSLGTSGVYFAVS+GFLS+PE AVHSFCHALP  WHLMSVML+AA
Sbjct: 240 AGAVGAGIVRHGQAMLSLGTSGVYFAVSDGFLSRPEQAVHSFCHALPGTWHLMSVMLNAA 299

Query: 296 SCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQ 355
           SCLD+ A+LTG ++V A++A AQ A    +   FLPYL+GERTPHN+  A G F GL   
Sbjct: 300 SCLDYTARLTGHADVGAMLAEAQAAPRRDDGPLFLPYLTGERTPHNDVHATGSFTGLQAD 359

Query: 356 HGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLD 415
               +LA A LEGVG  L DG++ V A G++   V +IGGG RS YW QMLADI+G+ L+
Sbjct: 360 TTRADLANATLEGVGLGLLDGIEAVDAAGLRADRVAVIGGGTRSAYWLQMLADIAGRPLE 419

Query: 416 YRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAY----QPR-RE 470
            R GGDVG ALGAARLA +AA P   + E+    PL   +LPDA R+A Y    QPR R+
Sbjct: 420 LRAGGDVGAALGAARLAHLAAEPGARIDEVCAMPPLVSEYLPDAARHAYYREHRQPRFRD 479

Query: 471 TFRRLYQQLLP 481
           T+RRL     P
Sbjct: 480 TYRRLRTATTP 490


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: 677
Number of extensions: 26
Number of successful extensions: 3
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: 490
Length adjustment: 34
Effective length of query: 450
Effective length of database: 456
Effective search space:   205200
Effective search space used:   205200
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 N515DRAFT_3230 N515DRAFT_3230 (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.27971.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.7e-173  563.5   0.0   2.1e-173  563.2   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230  N515DRAFT_3230 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3230  N515DRAFT_3230 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.2   0.0  2.1e-173  2.1e-173       1     477 [.       3     478 ..       3     483 .. 0.95

  Alignments for each domain:
  == domain 1  score: 563.2 bits;  conditional E-value: 2.1e-173
                                    TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakee.. 64 
                                                  lG+DlgTs+vKa+lvd+ g v a +s++ltv++p+p wsEqdp +w++a   a++ell++a+++  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230   3 LGLDLGTSAVKAVLVDAAGAVRAVASQPLTVSHPRPRWSEQDPVDWWRAAVAAIDELLQAAARDgi 68 
                                                  7*********************************************************99987633 PP

                                    TIGR01312  65 .kkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegf 129
                                                    ++++ai++sGQmHg++lLD +++vlrpaiLWnD r+ ++c+ +e  l+   ++++tgnla++gf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230  69 pASRVAAIGLSGQMHGATLLDRSDRVLRPAILWNDGRSDAQCRWMET-LP--DFHAITGNLAMPGF 131
                                                  3589**************************************98765.55..7************* PP

                                    TIGR01312 130 TapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkald 195
                                                  TapKl+Wvr+hep vf  +akvlLPkDylr+ Ltg++++++sDA+GTl++dv kr+ws+ +l+a+ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 132 TAPKLAWVREHEPSVFDAVAKVLLPKDYLRLCLTGDYASDVSDAAGTLWLDVGKRQWSDPMLAACG 197
                                                  ****************************************************************** PP

                                    TIGR01312 196 leesllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGv 261
                                                  l+++++P + e+se+aG++r+e+a+++G+ + v+vaaGggdnaagA+G+giv++g++++slGtSGv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 198 LSREQMPGVHEGSESAGRLRAELAERWGM-ARVPVAAGGGDNAAGAVGAGIVRHGQAMLSLGTSGV 262
                                                  *****************************.99********************************** PP

                                    TIGR01312 262 vlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevga 327
                                                  ++av+d   s pe+avhsFchalpg+w+ ++v+l+a+s+l+++++l+g+ dv ++++ea++++   
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 263 YFAVSDGFLSRPEQAVHSFCHALPGTWHLMSVMLNAASCLDYTARLTGHADVGAMLAEAQAAPRRD 328
                                                  ****************************************************************** PP

                                    TIGR01312 328 egvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkike 393
                                                  +g l+lPyl+GERtPh+d +a+gs++Gl+a+ttradla A+legv ++l d+++++ + +gl+ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 329 DGPLFLPYLTGERTPHNDVHATGSFTGLQADTTRADLANATLEGVGLGLLDGIEAVDA-AGLRADR 393
                                                  *********************************************************9.77***** PP

                                    TIGR01312 394 irliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkes 458
                                                  + +iGGG++s++w+q+ladi g++++ ++  + gaalGaA+lA +a++  + ++e+ ++    +e+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 394 VAVIGGGTRSAYWLQMLADIAGRPLELRAgGDVGAALGAARLAHLAAEPGARIDEVCAMPPLVSEY 459
                                                  *****************************99*****************777888877777766665 PP

                                    TIGR01312 459 vepiaenveayeelye.ryk 477
                                                    p+a++++ y+e  + r++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3230 460 -LPDAARHAYYREHRQpRFR 478
                                                  .6888888777765442555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (490 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: 7.84
//
[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