Alignments for a candidate for xylB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Dinoroseobacter shibae DFL-12

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate 3607827 Dshi_1235 xylulokinase (RefSeq)

Query= reanno::Smeli:SMc03164
         (484 letters)



>FitnessBrowser__Dino:3607827
          Length = 480

 Score =  351 bits (901), Expect = e-101
 Identities = 202/482 (41%), Positives = 261/482 (54%), Gaps = 10/482 (2%)

Query: 1   MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60
           M+LGLD+GTS VK ++ DG  R++G+AS  L V  P PG SEQDP  W R      A L 
Sbjct: 1   MFLGLDIGTSAVKGLVWDGA-RVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAEL- 58

Query: 61  ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALT 120
            +     A V  IGLSGQMHGA  L    AVLRP ILWND R+ REAA +   P   A  
Sbjct: 59  -SAQPGWAEVSAIGLSGQMHGAVCLGPDGAVLRPAILWNDNRAVREAAEMAALPGLAARV 117

Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180
           G    PGF APKLAW+   EPE+ A    V+  KD++ + L G  ++E S++AGT WLD 
Sbjct: 118 GVPPMPGFPAPKLAWLARTEPELHAATTMVMQAKDWVGMRLHGRAVTEYSEAAGTLWLDQ 177

Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240
             R W    LA + LE  QMP L  GTD AG L    AA  G+ PGV V  G GD    A
Sbjct: 178 AARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVIRGGGDAMVGA 237

Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300
            G+G V  GQA +SLGTSG    A+ ++ PNP   VH+F H +P  + QM  +L+    +
Sbjct: 238 AGIGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMAAMLNGAAPM 297

Query: 301 NWHSGVTGRSAAEL--TSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESS 358
            W +GV GRS  +L   +E  +    P    FLPYL+GERTPH D   R  F GL H S 
Sbjct: 298 AWLAGVLGRSVPDLLAAAETADPAHVP---LFLPYLTGERTPHGDPEARAGFEGLSHGSG 354

Query: 359 RAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLP 418
              + +AV++ ++++  D+   L  AG +     AIGGG+RS   L ++A  L +PV  P
Sbjct: 355 PGEMMRAVVDAIAYSFADAQAVLGEAGVRAASPLAIGGGARSDLVLQTLADVLEVPVQRP 414

Query: 419 ADGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYPA 478
           A  D G A GAA+L  + +     A +   PE      P  S    +     RYR LY  
Sbjct: 415 ASADLGPALGAAKLAAVGSGAMPAARLADPPEIGAVFHPRPS--ARHGARLARYRALYSE 472

Query: 479 IK 480
           ++
Sbjct: 473 LR 474


Lambda     K      H
   0.317    0.132    0.401 

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: 657
Number of extensions: 34
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: 480
Length adjustment: 34
Effective length of query: 450
Effective length of database: 446
Effective search space:   200700
Effective search space used:   200700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate 3607827 Dshi_1235 (xylulokinase (RefSeq))
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.12994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-134  435.6   0.0   1.2e-134  435.3   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607827  Dshi_1235 xylulokinase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607827  Dshi_1235 xylulokinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.3   0.0  1.2e-134  1.2e-134       1     452 [.       3     446 ..       3     475 .. 0.94

  Alignments for each domain:
  == domain 1  score: 435.3 bits;  conditional E-value: 1.2e-134
                         TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQm 77 
                                       lG+D+gTs+vK l+ d   +v++ +sa+l+v+ p pg sEqdpe+w++ +  +++el+++    ++e++ai++sGQm
  lcl|FitnessBrowser__Dino:3607827   3 LGLDIGTSAVKGLVWDG-ARVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAELSAQPG--WAEVSAIGLSGQM 76 
                                       7**************95.57**************************************9977..8************ PP

                         TIGR01312  78 HglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLP 154
                                       Hg+v L  +g vlrpaiLWnD r+++e++e+ +  g   l++++g  +++gf apKl+W+ + epe  a ++ v+  
  lcl|FitnessBrowser__Dino:3607827  77 HGAVCLGPDGAVLRPAILWNDNRAVREAAEMAALPG---LAARVGVPPMPGFPAPKLAWLARTEPELHAATTMVMQA 150
                                       *********************************999...99************************************ PP

                         TIGR01312 155 kDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkva 231
                                       kD++ ++L g++vteys A+GTl++d + r+w++e l+   le++++P+l ++++ aG +++++a++lGl+ gv+v+
  lcl|FitnessBrowser__Dino:3607827 151 KDWVGMRLHGRAVTEYSEAAGTLWLDQAARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVI 227
                                       ***************************************************************************** PP

                         TIGR01312 232 aGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkell 308
                                        Gggd ++gA G+g+v++g++++slGtSG +l+++++++++p+g vhsF+h++pg++ +++ +l+ ++ + wl+ +l
  lcl|FitnessBrowser__Dino:3607827 228 RGGGDAMVGAAGIGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMAAMLNGAAPMAWLAGVL 304
                                       ***************************************************************************** PP

                         TIGR01312 309 geldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegvafalrdsldilke 385
                                       g   v +l+++ae+++++ +  l+lPyl+GERtPh dp+ar+ + Gl++ +   +++rAv++++a++++d+  +l e
  lcl|FitnessBrowser__Dino:3607827 305 G-RSVPDLLAAAETADPA-HVPLFLPYLTGERTPHGDPEARAGFEGLSHGSGPGEMMRAVVDAIAYSFADAQAVLGE 379
                                       *.99**********9997.999******************************************************* PP

                         TIGR01312 386 lkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseav 452
                                        +g++ ++  +iGGGa+s++++q+lad+l+++v+ p+ ++ g+alGaA lAa+++g +  + +++   
  lcl|FitnessBrowser__Dino:3607827 380 -AGVRAASPLAIGGGARSDLVLQTLADVLEVPVQRPAsADLGPALGAAKLAAVGSGAMPAARLADPPE 446
                                       .67*********************************98999**************9766555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (480 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: 9.79
//
[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