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

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.19585.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.31
//
[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