Alignments for a candidate for xylB in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Acidovorax sp. GW101-3H11

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate Ac3H11_2937 Xylulose kinase (EC 2.7.1.17)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2937
          Length = 515

 Score =  448 bits (1152), Expect = e-130
 Identities = 247/513 (48%), Positives = 309/513 (60%), Gaps = 34/513 (6%)

Query: 1   MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60
           MYLG+DLGTSGVK +L++G Q ++ +A  A+   RP P WSEQ+PADW+ A E A+A+LR
Sbjct: 1   MYLGIDLGTSGVKLLLLNGAQTLVATADAAVPQHRPQPTWSEQNPADWMAAVEAAVAQLR 60

Query: 61  ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAAL-DGDPQFRAL 119
                A A VRGIGLSG MHGA +L     VLRP ILWND R+  E A L D  P  R +
Sbjct: 61  AQAPAAWAQVRGIGLSGHMHGAVVLGAQGHVLRPAILWNDGRASAECAQLEDAVPTSRQI 120

Query: 120 TGNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLD 179
           TGN+  PGFTAPKL W+R +EP +FA+VR VLLPKD+LRL LTG+ +S+MSD++GT WLD
Sbjct: 121 TGNLAMPGFTAPKLLWLRTHEPAVFAQVRTVLLPKDWLRLQLTGDAVSDMSDASGTLWLD 180

Query: 180 TGKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAAS 239
              R WS ++L A  L+   MP L EG+   GTLR ++A RWG+G GVVVA GAGDNAAS
Sbjct: 181 VQARTWSPAMLQACGLDVSHMPKLAEGSAPTGTLRSDVARRWGLGEGVVVAAGAGDNAAS 240

Query: 240 ACGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDA 299
           A G+G    GQ FVSLGTSGV+F    ++ P  E AVHAF HALP  WH M V+LSA  A
Sbjct: 241 AVGVGARTAGQGFVSLGTSGVVFRVTDAFAPATERAVHAFAHALPQRWHHMSVMLSAASA 300

Query: 300 LNWHSGVTGRS-AAELTSELG--ESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHE 356
             W + +TGRS  A+L+  +G   + +   +  FLPYLSGERTPHN+A   GVF GL  E
Sbjct: 301 FGWVTRLTGRSDEAQLSDAVGALSTSRQAQAPLFLPYLSGERTPHNNAAATGVFMGLRAE 360

Query: 357 SSRAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTA----------------------- 393
              A L  AV+EGV F + D L A+RAAG    R                          
Sbjct: 361 HEAADLAYAVMEGVGFGLLDGLNAMRAAGAGQGRAAGEAVGSTTPVQAELVEARTAPGAT 420

Query: 394 ------IGGGSRSRYWLSSIATALNLPVDLPADGDFGAAFGAARLGLIAATGADPAAVCT 447
                 +GGG+RS  W   +A+AL  P+  P      AA GAARL  +A  G D A  C 
Sbjct: 421 DSALALVGGGARSNPWAQLLASALGTPLQRPQGAHAAAALGAARLAAMAC-GGDEAHWCQ 479

Query: 448 APETAETIAPEASLVPAYEDAYQRYRRLYPAIK 480
                 T  P+ +      + Y R+  LYPA++
Sbjct: 480 PLPADATFMPQPAQQALLAERYARFVALYPALQ 512


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: 715
Number of extensions: 35
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 484
Length of database: 515
Length adjustment: 34
Effective length of query: 450
Effective length of database: 481
Effective search space:   216450
Effective search space used:   216450
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 Ac3H11_2937 (Xylulose kinase (EC 2.7.1.17))
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.8476.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.2e-162  527.8   2.7     5e-149  482.8   0.9    2.0  2  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937  Xylulose kinase (EC 2.7.1.17)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937  Xylulose kinase (EC 2.7.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.8   0.9    5e-149    5e-149       1     387 [.       3     389 ..       3     397 .. 0.98
   2 !   45.0   0.0   2.9e-16   2.9e-16     387     480 ..     417     508 ..     393     509 .. 0.84

  Alignments for each domain:
  == domain 1  score: 482.8 bits;  conditional E-value: 5e-149
                                        TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekak 62 
                                                      lGiDlgTs+vK ll++  ++++a++ a+++  +p+p+wsEq+p +w++a+e a+++l+++a 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937   3 LGIDLGTSGVKLLLLNGAQTLVATADAAVPQHRPQPTWSEQNPADWMAAVEAAVAQLRAQAP 64 
                                                      7************************************************************* PP

                                        TIGR01312  63 eekkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnl 124
                                                        ++++++i++sG mHg+v+L ++g+vlrpaiLWnD r+++ec++le++++  +++++tgnl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937  65 AAWAQVRGIGLSGHMHGAVVLGAQGHVLRPAILWNDGRASAECAQLEDAVP--TSRQITGNL 124
                                                      **************************************************9..99******* PP

                                        TIGR01312 125 alegfTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrew 186
                                                      a++gfTapKllW+r hep vfa++++vlLPkD+lr++Ltg++v+++sDAsGTl++dv+ r+w
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 125 AMPGFTAPKLLWLRTHEPAVFAQVRTVLLPKDWLRLQLTGDAVSDMSDASGTLWLDVQARTW 186
                                                      ************************************************************** PP

                                        TIGR01312 187 skellkaldleesllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivk 248
                                                      s ++l+a+ l+ s +Pkl e+s+ +G++r++va+++Gl egv vaaG+gdnaa+A+G+g+ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 187 SPAMLQACGLDVSHMPKLAEGSAPTGTLRSDVARRWGLGEGVVVAAGAGDNAASAVGVGART 248
                                                      ************************************************************** PP

                                        TIGR01312 249 egkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellge 310
                                                      +g+ +vslGtSGvv+ v+d+  + +e avh+F+halp++w++++v+lsa+sa  w+++l+g+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 249 AGQGFVSLGTSGVVFRVTDAFAPATERAVHAFAHALPQRWHHMSVMLSAASAFGWVTRLTGR 310
                                                      *************************************************************9 PP

                                        TIGR01312 311 ldveelneeaekvevg..aegvlllPylsGERtPhldpqargsliGltanttradlarAvle 370
                                                      +d ++l  ++ + +++  a++ l+lPylsGERtPh++++a+g+++Gl+a+++ adla+Av+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 311 SDEAQLSDAVGALSTSrqAQAPLFLPYLSGERTPHNNAAATGVFMGLRAEHEAADLAYAVME 372
                                                      9999**9999887665559******************************************* PP

                                        TIGR01312 371 gvafalrdsldilkelk 387
                                                      gv f+l d+l+++++++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 373 GVGFGLLDGLNAMRAAG 389
                                                      **************966 PP

  == domain 2  score: 45.0 bits;  conditional E-value: 2.9e-16
                                        TIGR01312 387 kglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAaialgekdlvee 447
                                                       g + + + l+GGGa+s+ w q+la  lg++++ p+ ++ +aalGaA+lAa+a+g  d+++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 417 PGATDSALALVGGGARSNPWAQLLASALGTPLQRPQgAHAAAALGAARLAAMACGG-DEAHW 477
                                                      556678899***************************7788899***********96.68999 PP

                                        TIGR01312 448 cseavvkqkesvepiaenveayeelyerykkly 480
                                                      c+   ++++    p+ ++++  +e+y+r+ +ly
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2937 478 CQPLPADATFM--PQPAQQALLAERYARFVALY 508
                                                      98887777766..77777778999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (515 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: 0.08u 0.01s 00:00:00.09 Elapsed: 00:00:00.07
# Mc/sec: 3.12
//
[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