Alignments for a candidate for xylB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Stenotrophomonas chelatiphaga DSM 21508

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_083491975.1 ABB28_RS08205 xylulokinase

Query= reanno::pseudo6_N2E2:Pf6N2E2_805
         (495 letters)



>NCBI__GCF_001431535.1:WP_083491975.1
          Length = 526

 Score =  403 bits (1036), Expect = e-117
 Identities = 215/483 (44%), Positives = 287/483 (59%), Gaps = 4/483 (0%)

Query: 6   LFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQATHQA 65
           ++LGID GTQ  K L  D  + +V+G  + + ++ S  +G REQD   W+ A        
Sbjct: 32  VYLGIDAGTQSLKVLAYDPAAREVVGQQSRSLALDSADDGSREQDAASWIRALQDCV--- 88

Query: 66  LAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHLGGEDG 125
           LA        + G+ VSGQQHGLV L     VL P KLWCDT +T + D + A +GGE  
Sbjct: 89  LALPEAVRARVGGLAVSGQQHGLVALAADDSVLAPVKLWCDTSSTAQCDAITAAVGGESA 148

Query: 126 SLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYGDASGT 185
            +   G  +  GYT SKL WT++  PQ +  +  + LPHD+LN WLTG    E GDASGT
Sbjct: 149 CIAAAGNPLRVGYTASKLPWTKQHRPQAYASLDGIALPHDYLNLWLTGARFMECGDASGT 208

Query: 186 GYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEAVVASG 245
           G+ +VR RQW  Q+L   DP   L   LP L+ A      +LPA+AA LG+     VA G
Sbjct: 209 GWLDVRARQWSPQMLAATDPDRDLAGLLPPLV-APDTTFALLPAVAAALGLPAGIRVAVG 267

Query: 246 GGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWLPLICT 305
           GGDNMM AIGTG ++ G ++MSLG+SGT++A++A P + PQ   A FC+S GGWLPLICT
Sbjct: 268 GGDNMMAAIGTGAVREGRLSMSLGTSGTLFAWSARPKIDPQGRWAAFCASDGGWLPLICT 327

Query: 306 MNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGSLLGLT 365
           MN T AT  +  LL +  D   AL+  +  GA G+ +LPF NGER P LP A G+L G+ 
Sbjct: 328 MNCTVATNQVAALLGIQHDQTEALLQASLPGAAGLVLLPFFNGERSPDLPLAKGALHGMD 387

Query: 366 TTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVADTMDT 425
             NL+ ANL RA +EG ++ L+ G D L   GLQ   + L GGG+ SA WRQ++AD    
Sbjct: 388 LHNLSPANLYRAAMEGASYSLKLGYDALHEAGLQGARVVLTGGGANSAAWRQLIADLFQL 447

Query: 426 TVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAASQQAY 485
            V    Q+E AA GAA+QAAW  +G+   LA+L +  V  DP+   +P     A+  + Y
Sbjct: 448 PVEVPVQAEGAAFGAALQAAWACAGASMPLADLVDAHVVFDPALSAQPDPVRGASYARGY 507

Query: 486 ERY 488
           +R+
Sbjct: 508 QRF 510


Lambda     K      H
   0.318    0.133    0.402 

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: 730
Number of extensions: 38
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: 495
Length of database: 526
Length adjustment: 34
Effective length of query: 461
Effective length of database: 492
Effective search space:   226812
Effective search space used:   226812
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 WP_083491975.1 ABB28_RS08205 (xylulokinase)
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.30254.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-152  493.1   0.0   4.2e-152  492.9   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_083491975.1  ABB28_RS08205 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_083491975.1  ABB28_RS08205 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.9   0.0  4.2e-152  4.2e-152       1     479 [.      34     513 ..      34     515 .. 0.97

  Alignments for each domain:
  == domain 1  score: 492.9 bits;  conditional E-value: 4.2e-152
                                 TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkei 68 
                                               lGiD gT+s+K+l +d + +ev++++s sl++ s  +g +Eqd  +w++al++++ +l e+ +   +++
  lcl|NCBI__GCF_001431535.1:WP_083491975.1  34 LGIDAGTQSLKVLAYDpAAREVVGQQSRSLALDSADDGSREQDAASWIRALQDCVLALPEAVR---ARV 99 
                                               7***********************************************************988...79* PP

                                 TIGR01312  69 kaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlalegfTapKllW 136
                                                ++++sGQ+Hglv+L +++ vl p++LW+Dt ++++c+ +++++g e+++++++gn    g+Ta+Kl W
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 100 GGLAVSGQQHGLVALAADDSVLAPVKLWCDTSSTAQCDAITAAVGgESACIAAAGNPLRVGYTASKLPW 168
                                               *********************************************9*********************** PP

                                 TIGR01312 137 vrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldle...esllP 202
                                               +++h+p+++a ++ + LP+Dyl+++Ltg   +e +DAsGT+++dv+ r+ws ++l+a+d++     llP
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 169 TKQHRPQAYASLDGIALPHDYLNLWLTGARFMECGDASGTGWLDVRARQWSPQMLAATDPDrdlAGLLP 237
                                               *************************************************************555568** PP

                                 TIGR01312 203 klvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaes 271
                                                lv+++ + + + ++va++lGl +g++va Gggdn+++AiG+g+v+eg +++slGtSG+++a + +++ 
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 238 PLVAPDTTFA-LLPAVAAALGLPAGIRVAVGGGDNMMAAIGTGAVREGRLSMSLGTSGTLFAWSARPKI 305
                                               *****98886.5566****************************************************** PP

                                 TIGR01312 272 dpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGER 340
                                               dp+g+ ++Fc +  g+w+pl++t+++t a++ +++llg ++ ++++++ +++ +ga g++llP+++GER
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 306 DPQGRWAAFCASD-GGWLPLICTMNCTVATNQVAALLG-IQHDQTEALLQASLPGAAGLVLLPFFNGER 372
                                               *************.************************.****************************** PP

                                 TIGR01312 341 tPhldpqargsliGlt.anttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrq 408
                                                P l p a+g l+G++ +n + a+l rA++eg++++l+ + d+l+e +gl+ ++++l+GGGa s++wrq
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 373 SPDL-PLAKGALHGMDlHNLSPANLYRAAMEGASYSLKLGYDALHE-AGLQGARVVLTGGGANSAAWRQ 439
                                               ****.*****************************************.67******************** PP

                                 TIGR01312 409 iladilglevvvpeeeegaalGaAilAaialg..ekdlveecseavvkqkes.vepiaenveayeelye 474
                                               ++ad+++l+v+vp ++egaa+GaA +Aa+a+    + l+++++++vv + +  ++p+  + ++y++ y+
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 440 LIADLFQLPVEVPVQAEGAAFGAALQAAWACAgaSMPLADLVDAHVVFDPALsAQPDPVRGASYARGYQ 508
                                               ******************************997777899*******9999988**************** PP

                                 TIGR01312 475 rykkl 479
                                               r+ + 
  lcl|NCBI__GCF_001431535.1:WP_083491975.1 509 RFVHY 513
                                               *9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (526 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: 10.22
//
[ok]

This GapMind analysis is from Sep 24 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