Alignments for a candidate for xylB in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Pseudomonas simiae WCS417

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate GFF2677 PS417_13655 xylulose kinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__WCS417:GFF2677
          Length = 496

 Score =  400 bits (1028), Expect = e-116
 Identities = 215/479 (44%), Positives = 296/479 (61%), Gaps = 14/479 (2%)

Query: 3   IGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQ 62
           +GIDLGTS +K IL++  G V+A    +L+VSR +  WSEQDP+ WWQA  +A+  L   
Sbjct: 7   LGIDLGTSELKAILMDLDGSVLAHAGVRLSVSRRNSGWSEQDPQDWWQACLQALAQLRTH 66

Query: 63  HSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITGNL 122
            +   V  +G++GQMHGA LL A  RVL PAILW+D R   E   L         +TG+L
Sbjct: 67  EAFARVACIGLSGQMHGAVLLGADNRVLYPAILWDDSRAVAEAERLGTAFAD---VTGSL 123

Query: 123 MMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKR 182
            M G TAPKLLW+++HEP++F+ ID VL PKDYLRLR++GE  S+MSDAAGT+WLDVA+R
Sbjct: 124 PMAGLTAPKLLWLKQHEPQVFKAIDCVLSPKDYLRLRLSGERISEMSDAAGTLWLDVARR 183

Query: 183 DWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVA-GGGDNAAGAVGV 241
           +W   ML+A  LS  QMP L EG   +  L        G+++  V+A GGGDN   AVG+
Sbjct: 184 EWFVPMLRATGLSPAQMPRLVEGGAASAVL---TVDGLGLSSSVVIAGGGGDNPVAAVGI 240

Query: 242 GMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWA 301
           G + A  A ++LGTS    A+++     P SAVHSFCHALP RW+ M  ML+ ASCL W 
Sbjct: 241 GAIKAGDAFITLGTSAAIVAITDHAAGNPASAVHSFCHALPNRWYTMGAMLAGASCLRWV 300

Query: 302 AKLTGLSNVPALI--AAAQQADESAEPV---WFLPYLSGERTPHNNPQAKGVFFGLTHQH 356
            +LTG+ +   L+    AQ   + A P+    FLPYL+GERTPHN+P  +G F GL H  
Sbjct: 301 TRLTGMPDEQTLLDQVQAQLPIKQAVPLSTPLFLPYLAGERTPHNDPLLRGGFMGLGHDC 360

Query: 357 GPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDY 416
            P  L  AV+EGVG+ L D +  V + G    +  L+GGGARSEYW Q+LA+I  +++  
Sbjct: 361 TPAMLGYAVMEGVGFGLLDALRAVQSAGANVDACALVGGGARSEYWAQLLANILQREIYT 420

Query: 417 RTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRL 475
             G ++   +GAA+L  ++     +L++    +P++  + PD+ + A    R   F+ L
Sbjct: 421 LHGSELSACIGAAKLGFLSIGEGDALLQ--AGMPVKARYRPDSAQQAVLAARYRLFQGL 477


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: 619
Number of extensions: 27
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: 496
Length adjustment: 34
Effective length of query: 450
Effective length of database: 462
Effective search space:   207900
Effective search space used:   207900
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 GFF2677 PS417_13655 (xylulose kinase)
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.19864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-145  469.4   0.0   6.4e-145  469.2   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF2677  PS417_13655 xylulose kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2677  PS417_13655 xylulose kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.2   0.0  6.4e-145  6.4e-145       1     479 [.       7     477 ..       7     479 .. 0.92

  Alignments for each domain:
  == domain 1  score: 469.2 bits;  conditional E-value: 6.4e-145
                           TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisG 75 
                                         lGiDlgTs++Ka+l+d  g+v+a++  +l+v++ ++gwsEqdp++w++a+ +al++l+++ +   ++++ i++sG
  lcl|FitnessBrowser__WCS417:GFF2677   7 LGIDLGTSELKAILMDLDGSVLAHAGVRLSVSRRNSGWSEQDPQDWWQACLQALAQLRTHEA--FARVACIGLSG 79 
                                         7********************************************************99966..8********** PP

                           TIGR01312  76 QmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfariak 150
                                         QmHg+vlL ++++vl+paiLW D r+++e+e+l  +     ++++tg+l+++g+TapKllW+++hep+vf+ i+ 
  lcl|FitnessBrowser__WCS417:GFF2677  80 QMHGAVLLGADNRVLYPAILWDDSRAVAEAERLGTA-----FADVTGSLPMAGLTAPKLLWLKQHEPQVFKAIDC 149
                                         ******************************988665.....57******************************** PP

                           TIGR01312 151 vlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreevakklGle 225
                                         vl PkDylr++L ge ++e+sDA+GTl++dv++rew   +l+a+ l+++++P+lve+ + ++ ++    + lGl+
  lcl|FitnessBrowser__WCS417:GFF2677 150 VLSPKDYLRLRLSGERISEMSDAAGTLWLDVARREWFVPMLRATGLSPAQMPRLVEGGAASAVLTV---DGLGLS 221
                                         **********************************************************99999887...89**** PP

                           TIGR01312 226 egvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsa 300
                                         ++v +a+Gggdn ++A+G+g++k+g++++ lGtS  ++a++d+a  +p++avhsFchalp++wy++g +l+ +s+
  lcl|FitnessBrowser__WCS417:GFF2677 222 SSVVIAGGGGDNPVAAVGIGAIKAGDAFITLGTSAAIVAITDHAAGNPASAVHSFCHALPNRWYTMGAMLAGASC 296
                                         *************************************************************************** PP

                           TIGR01312 301 lewlkellgeldveelneeaekvevg.....aegvlllPylsGERtPhldpqargsliGltanttradlarAvle 370
                                         l w+++l+g  d ++l+ ++++  +          l+lPyl GERtPh+dp  rg ++Gl ++ t a l +Av+e
  lcl|FitnessBrowser__WCS417:GFF2677 297 LRWVTRLTGMPDEQTLLDQVQAQLPIkqavpLSTPLFLPYLAGERTPHNDPLLRGGFMGLGHDCTPAMLGYAVME 371
                                         *********8888888877765433301111345689************************************** PP

                           TIGR01312 371 gvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdl 444
                                         gv f+l d+l ++++ +g +++ + l+GGGa+se+w q+la+il++e+ + + +e  a +GaA l+ ++ ge   
  lcl|FitnessBrowser__WCS417:GFF2677 372 GVGFGLLDALRAVQS-AGANVDACALVGGGARSEYWAQLLANILQREIYTLHgSELSACIGAAKLGFLSIGEG-- 443
                                         ***************.67********************************9956667789**********975.. PP

                           TIGR01312 445 veecseavvkqkesvepiaenveayeelyerykkl 479
                                          + + +a +  k++++p+ ++++  + +y  ++ l
  lcl|FitnessBrowser__WCS417:GFF2677 444 -DALLQAGMPVKARYRPDSAQQAVLAARYRLFQGL 477
                                         .4555666666667788888888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (496 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: 10.75
//
[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