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 Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate GFF2488 PS417_12690 xylulose kinase

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



>FitnessBrowser__WCS417:GFF2488
          Length = 493

 Score =  813 bits (2099), Expect = 0.0
 Identities = 402/495 (81%), Positives = 440/495 (88%), Gaps = 2/495 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           M  Q LFLGIDCGTQGTKA++LDA+SG+VLGLGAAAH++ISGANGRREQ TQ+WLDAFT+
Sbjct: 1   MTQQNLFLGIDCGTQGTKAIVLDASSGKVLGLGAAAHTLISGANGRREQHTQEWLDAFTE 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           ATH+AL  AGVDGQ ILGIGVSGQQHGLVLLDDQG+VLRPAKLWCDTET PEN+RLL HL
Sbjct: 61  ATHRALQQAGVDGQDILGIGVSGQQHGLVLLDDQGRVLRPAKLWCDTETAPENERLLQHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSLERLGV IAPGYTVSKLLWTREQHP +F RI  +LLPHD+LNYWLTGR  +EYG
Sbjct: 121 GGESGSLERLGVAIAPGYTVSKLLWTREQHPDIFARITHILLPHDYLNYWLTGRAVAEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVRTR+WDV LL+HIDPS RL+ ALP+LIEA Q VG ILPAIA  LGINP A
Sbjct: 181 DASGTGYFNVRTREWDVALLKHIDPSGRLENALPQLIEADQSVGTILPAIAERLGINPNA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           +V+SGGGDNMMGAIGTGNI PGVITMSLGSSGTVYA+A +P+VSPQ SVATFCSSSGGWL
Sbjct: 241 IVSSGGGDNMMGAIGTGNIAPGVITMSLGSSGTVYAFADQPSVSPQASVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNATG IREL DLD+ AFNALV +APIGA+GV MLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATGVIRELFDLDLTAFNALVEQAPIGADGVSMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           L GLT TNLTRANLCRAVVEGTTFGLRYGLDLLR  GLQ+QSIRLIGGGSKS  WRQ+VA
Sbjct: 361 LHGLTMTNLTRANLCRAVVEGTTFGLRYGLDLLRQTGLQSQSIRLIGGGSKSPIWRQMVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480
           D M+T V+CTEQSEAAALGAAIQAAW  SG    LA LC++CV +DP+S T P+AA V+A
Sbjct: 421 DIMNTEVVCTEQSEAAALGAAIQAAWSQSGE--SLASLCDKCVSVDPASRTLPVAASVSA 478

Query: 481 SQQAYERYRQHVATL 495
            QQAYERY+Q VATL
Sbjct: 479 YQQAYERYQQLVATL 493


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: 901
Number of extensions: 34
Number of successful extensions: 2
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: 493
Length adjustment: 34
Effective length of query: 461
Effective length of database: 459
Effective search space:   211599
Effective search space used:   211599
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 GFF2488 PS417_12690 (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.680720.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-195  636.6   0.0   1.3e-195  636.4   0.0    1.0  1  FitnessBrowser__WCS417:GFF2488  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF2488  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.4   0.0  1.3e-195  1.3e-195       1     480 [.       8     490 ..       8     491 .. 0.99

  Alignments for each domain:
  == domain 1  score: 636.4 bits;  conditional E-value: 1.3e-195
                       TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisisGQmH 78 
                                     lGiD+gT+++Ka+++d ++g+v++ g+a++t+is ++g++Eq+++ewl+a++ea++++l++a ++ ++i +i++sGQ+H
  FitnessBrowser__WCS417:GFF2488   8 LGIDCGTQGTKAIVLDaSSGKVLGLGAAAHTLISGANGRREQHTQEWLDAFTEATHRALQQAGVDGQDILGIGVSGQQH 86 
                                     7***************99************************************************************* PP

                       TIGR01312  79 glvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlalegfTapKllWvrkhepevfariakvlLPkD 156
                                     glvlLD++g+vlrpa+LW+Dt+ta e+e+l ++lg e+ +le++g ++++g+T++KllW+r+++p++fari+++lLP+D
  FitnessBrowser__WCS417:GFF2488  87 GLVLLDDQGRVLRPAKLWCDTETAPENERLLQHLGgESGSLERLGVAIAPGYTVSKLLWTREQHPDIFARITHILLPHD 165
                                     ***********************************9******************************************* PP

                       TIGR01312 157 ylrykLtgevvteysDAsGTllfdvkkrewskellkaldle...esllPklvessekaGkvreevakklGleegvkvaa 232
                                     yl+y+Ltg++v+ey+DAsGT++f+v++rew+ +llk++d++   e++lP+l+e+++++G++ +++a++lG++ + +v++
  FitnessBrowser__WCS417:GFF2488 166 YLNYWLTGRAVAEYGDASGTGYFNVRTREWDVALLKHIDPSgrlENALPQLIEADQSVGTILPAIAERLGINPNAIVSS 244
                                     *****************************************9999********************************** PP

                       TIGR01312 233 GggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgel 311
                                     Gggdn++gAiG+g++++g++++slG+SG+v+a++d+++++p+++v++Fc+++ g+w+pl++t+++t+a+ +++el+  l
  FitnessBrowser__WCS417:GFF2488 245 GGGDNMMGAIGTGNIAPGVITMSLGSSGTVYAFADQPSVSPQASVATFCSSS-GGWLPLICTMNLTNATGVIRELFD-L 321
                                     ****************************************************.************************.* PP

                       TIGR01312 312 dveelneeaekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrdsldilkelkgl 389
                                     d++++n+++e++++ga+gv++lP+l+GER+P+l p+a+gsl+Glt +n tra+l+rAv+eg++f+lr++ld+l++ +gl
  FitnessBrowser__WCS417:GFF2488 322 DLTAFNALVEQAPIGADGVSMLPFLNGERVPAL-PHATGSLHGLTmTNLTRANLCRAVVEGTTFGLRYGLDLLRQ-TGL 398
                                     *********************************.***********8999**************************.77* PP

                       TIGR01312 390 kikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialgekdlveecseavvkqkes.vepiaenve 467
                                     ++++irliGGG+ks++wrq++adi+++evv++e++e+aalGaAi+Aa++++ ++l+++c+++v+ + +s + p+a++v+
  FitnessBrowser__WCS417:GFF2488 399 QSQSIRLIGGGSKSPIWRQMVADIMNTEVVCTEQSEAAALGAAIQAAWSQSGESLASLCDKCVSVDPASrTLPVAASVS 477
                                     ***************************************************999************9999********* PP

                       TIGR01312 468 ayeelyerykkly 480
                                     ay+++yery++l+
  FitnessBrowser__WCS417:GFF2488 478 AYQQAYERYQQLV 490
                                     **********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (493 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.23
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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