GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Bacteroides thetaiotaomicron VPI-5482

Align Xylulose kinase; Short=Xylulokinase; EC 2.7.1.17 (characterized, see rationale)
to candidate 353949 BT4423 xylulose kinase (NCBI ptt file)

Query= uniprot:Q97FW4
         (500 letters)



>FitnessBrowser__Btheta:353949
          Length = 505

 Score =  331 bits (848), Expect = 4e-95
 Identities = 173/493 (35%), Positives = 279/493 (56%), Gaps = 5/493 (1%)

Query: 3   YLLGIDVGTSGTKTALFDECGNTIKTSTHEYELFQPQVGWAEQNPENWWTACVKGIREVI 62
           Y+L  D+GTSG K  LFDE G  I + T  Y         AEQNP +WW A V   + ++
Sbjct: 2   YILAHDLGTSGNKATLFDESGLLIASRTAAYPTDYASGNRAEQNPHHWWKAIVDTTQALL 61

Query: 63  EKSKIDPLDIKGIGISGQMHGLVLIDKEYKVIRNSIIWCDQRTEKECTQITDTIGKEKLI 122
           E   + P DI G+ +SGQM G + IDK+   +R  +++CDQR+++E  ++T+ I      
Sbjct: 62  EL--VSPNDIAGVALSGQMMGCLCIDKDGNPLRPHMLYCDQRSQEEEAKLTEKIDPLHFY 119

Query: 123 RITGNPALTGFTLSKLLWVRNNEPDNYKRIYKVLLPKDYIRFKLTGVFAAEVSDASGTQM 182
            ITG+     +++ KL+WV+ +EP+ + +  K+L  KDYI ++L G  A + SDASGT  
Sbjct: 120 EITGHRISASYSVEKLMWVKKHEPEIFAQTAKMLNAKDYINYRLCGTIATDPSDASGTNA 179

Query: 183 LDINTRNWSEELLDDLRIDKNILPDVYESVVVSGCVIEKASKETKLAVNTPVVGGAGDQA 242
            D+N   WSEE+++   +D ++ P+V  S+ V G +  +A++ET L   TPV+ G GD +
Sbjct: 180 YDLNRWQWSEEIIEAAELDLSLFPEVRSSIDVIGEITNEAARETGLLAGTPVICGGGDGS 239

Query: 243 AGAIGNGIVREGLISTVIGTSGVVFAATDTPRFDSKGRVHTLCHAVPNKWHIMGVTQGAG 302
              +G G V  G     +G+S  V    + P  D + R     H VP   H  G  Q AG
Sbjct: 240 CAGVGVGCVAPGTAYNYLGSSSWVALTVEKPIVDEQRRTMNWAHVVPGMLHPSGTMQAAG 299

Query: 303 LSLNWFKRTFCAKEILESKEAGINIYDLLTEKASQSKPGSNGIIYLPYLMGERTPHIDPN 362
            S NW     C  E   + ++G ++++L+ E+   S  G+N +++LPY++GERTP  + +
Sbjct: 300 SSYNWMINQLCQNEQALAAQSGRSVFELIDEQIIASPIGANKLLFLPYMLGERTPRWNVD 359

Query: 363 VKGAFLGISLINNHNDFVRSILEGVGFSLKNCLDIIENMKVNIEEIRVSGGGAESSIWRQ 422
            KGAF+G++L + H D +R+++EGV  +L   ++I     V I+ + V GG A++ +WRQ
Sbjct: 360 AKGAFIGLTLGHKHGDMLRAVMEGVTLNLGFIINIFRK-HVPIDRMTVIGGCAQNPVWRQ 418

Query: 423 ILSDIFNYELTTVK-ASEGPALGVAILAGVGAGIYNSVEEACDKIVKGNEKVMPNANLIE 481
           +++DI+  E+       E  ++G AILAG+GAG++       D+ V+  + V P    ++
Sbjct: 419 MMADIYQAEIRVPNYLEEATSMGAAILAGIGAGVFPDF-SVIDRFVRIEQTVQPIPENVK 477

Query: 482 VYSKVYEVYNSAY 494
            Y     V++ AY
Sbjct: 478 KYEAWMPVFDQAY 490


Lambda     K      H
   0.317    0.136    0.404 

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: 612
Number of extensions: 27
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: 500
Length of database: 505
Length adjustment: 34
Effective length of query: 466
Effective length of database: 471
Effective search space:   219486
Effective search space used:   219486
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate 353949 BT4423 (xylulose kinase (NCBI ptt file))
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.2884.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-126  408.7   0.0   1.8e-126  408.4   0.0    1.0  1  lcl|FitnessBrowser__Btheta:353949  BT4423 xylulose kinase (NCBI ptt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353949  BT4423 xylulose kinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.4   0.0  1.8e-126  1.8e-126       4     480 ..       7     490 ..       4     491 .. 0.96

  Alignments for each domain:
  == domain 1  score: 408.4 bits;  conditional E-value: 1.8e-126
                          TIGR01312   4 DlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmHg 79 
                                        DlgTs+ Ka l de+g +ias +a++++   + +++Eq+p++w++a+ +++++lle  +  +++i+++++sGQm g
  lcl|FitnessBrowser__Btheta:353949   7 DLGTSGNKATLFDESGLLIASRTAAYPTDYASGNRAEQNPHHWWKAIVDTTQALLELVS--PNDIAGVALSGQMMG 80 
                                        9********************************************************77..8************** PP

                          TIGR01312  80 lvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariakvlLPk 155
                                           +D++g++lrp +L++D+r++ee ++l+e++   ++ e+tg  + +++ + Kl+Wv+khepe+fa++ak+l  k
  lcl|FitnessBrowser__Btheta:353949  81 CLCIDKDGNPLRPHMLYCDQRSQEEEAKLTEKIDPLHFYEITGHRISASYSVEKLMWVKKHEPEIFAQTAKMLNAK 156
                                        **********************************99**************************************** PP

                          TIGR01312 156 DylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGleegvkva 231
                                        Dy++y+L g+++t+ sDAsGT  +d ++ +ws+e+++a++l+ sl+P++ +s +++G++++e+a+++Gl +g++v+
  lcl|FitnessBrowser__Btheta:353949 157 DYINYRLCGTIATDPSDASGTNAYDLNRWQWSEEIIEAAELDLSLFPEVRSSIDVIGEITNEAARETGLLAGTPVI 232
                                        **************************************************************************** PP

                          TIGR01312 232 aGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkel 307
                                        +Gggd  ++ +G+g v++g++   lG+S  v  + +k+ +d++ +  +++h++pg  +p g + +a+s+ +w+ + 
  lcl|FitnessBrowser__Btheta:353949 233 CGGGDGSCAGVGVGCVAPGTAYNYLGSSSWVALTVEKPIVDEQRRTMNWAHVVPGMLHPSGTMQAAGSSYNWMINQ 308
                                        ************************************************************************9987 PP

                          TIGR01312 308 lg...........eldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradlarAvlegv 372
                                        l            ++ +e ++e++ ++++ga+ +l+lPy+ GERtP  + +a+g +iGlt  +++ d+ rAv+egv
  lcl|FitnessBrowser__Btheta:353949 309 LCqneqalaaqsgRSVFELIDEQIIASPIGANKLLFLPYMLGERTPRWNVDAKGAFIGLTLGHKHGDMLRAVMEGV 384
                                        76455555555444567889999***************************************************** PP

                          TIGR01312 373 afalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlvee 447
                                        ++ l   ++i+++ + ++i+++++iGG a+++vwrq++adi ++e++vp+  ee++++GaAilA i++g + ++++
  lcl|FitnessBrowser__Btheta:353949 385 TLNLGFIINIFRK-H-VPIDRMTVIGGCAQNPVWRQMMADIYQAEIRVPNyLEEATSMGAAILAGIGAGVFPDFSV 458
                                        *************.4.9*********************************99*******************99999 PP

                          TIGR01312 448 cseavvkqkesvepiaenveayeelyerykkly 480
                                        ++++v   +++v+pi env++ye  + ++ + y
  lcl|FitnessBrowser__Btheta:353949 459 IDRFVRI-EQTVQPIPENVKKYEAWMPVFDQAY 490
                                        9887655.5566***********9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (505 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: 00:00:00.01
# Mc/sec: 12.54
//
[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:

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