Alignments for a candidate for xylB in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Pseudomonas fluorescens GW456-L13

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate PfGW456L13_3037 Xylulose kinase (EC 2.7.1.17)

Query= reanno::pseudo5_N2C3_1:AO356_27695
         (495 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037
          Length = 498

 Score =  816 bits (2108), Expect = 0.0
 Identities = 406/498 (81%), Positives = 443/498 (88%), Gaps = 3/498 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           M   QLFLGIDCGTQGTKA+ILD+ +G+VLGQG A+HS+ISG NGRREQDTQQWL+AF  
Sbjct: 1   MTTLQLFLGIDCGTQGTKAIILDSANGEVLGQGTASHSLISGPNGRREQDTQQWLEAFAT 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYL 120
           AT +AL AA  +GQ+ILGIGVSGQQHGLVLLDDQG+VLR AKLWCDTETTPENDRLLA+L
Sbjct: 61  ATRRALLAAKTNGQSILGIGVSGQQHGLVLLDDQGKVLRAAKLWCDTETTPENDRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSL+RLGVVIAPGYT+SKLLWT+EQHP+VF RI+ +LLPHD+LN+WLTGR CSEYG
Sbjct: 121 GGEKGSLKRLGVVIAPGYTLSKLLWTKEQHPEVFSRISRILLPHDYLNHWLTGRSCSEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDA 240
           DASGTGYFNVRTRQWD QLL+ IDPS RLQAALPELI  HQ VG ILP IA HLGINP A
Sbjct: 181 DASGTGYFNVRTRQWDGQLLRDIDPSGRLQAALPELIAPHQAVGTILPGIAEHLGINPRA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWL 300
           +V+SGGGDNMMGAIGTGNIQPG ITMSLGSSGTVYAYA +P V+   +VATFCSS+GGWL
Sbjct: 241 LVSSGGGDNMMGAIGTGNIQPGAITMSLGSSGTVYAYADQPNVATDAAVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATAS 360
           PLICTMNLTNAT  IRELLDLDID FN LV QAPIGA+GVCMLPF NGERVPALPHA+AS
Sbjct: 301 PLICTMNLTNATSLIRELLDLDIDQFNDLVAQAPIGADGVCMLPFFNGERVPALPHASAS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVA 420
           L GLT TNLTRANLCRAVVEGTTFGLRYGLDLLR NGL+++SIRLIGGGSKS VWRQIVA
Sbjct: 361 LSGLTMTNLTRANLCRAVVEGTTFGLRYGLDLLRRNGLQSRSIRLIGGGSKSAVWRQIVA 420

Query: 421 DIMDTTVICTEQSEAAALGAAIQAAWCHS---GAQDSLAELCERCVKLDPASETRPVTAH 477
           D M+T VICTEQSEAAALGAAIQAAWC S   G +DSLA+LCERCVKLDPASET PV  +
Sbjct: 421 DTMNTPVICTEQSEAAALGAAIQAAWCVSRANGHEDSLAQLCERCVKLDPASETLPVADN 480

Query: 478 VTASQQAYERYRQHVATL 495
           V A QQAYERY+QHVATL
Sbjct: 481 VQACQQAYERYQQHVATL 498


Lambda     K      H
   0.319    0.134    0.405 

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: 903
Number of extensions: 33
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: 498
Length adjustment: 34
Effective length of query: 461
Effective length of database: 464
Effective search space:   213904
Effective search space used:   213904
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 PfGW456L13_3037 (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.22845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.4e-184  600.0   0.0   1.6e-184  599.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037  Xylulose kinase (EC 2.7.1.17)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037  Xylulose kinase (EC 2.7.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  599.8   0.0  1.6e-184  1.6e-184       1     480 [.       8     495 ..       8     496 .. 0.98

  Alignments for each domain:
  == domain 1  score: 599.8 bits;  conditional E-value: 1.6e-184
                                               TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeeal 54 
                                                             lGiD+gT+++Ka+++d ++gev+++g+as+++is  +g++Eqd+++wlea+ +a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037   8 LGIDCGTQGTKAIILDsANGEVLGQGTASHSLISGPNGRREQDTQQWLEAFATAT 62 
                                                             7****************************************************** PP

                                               TIGR01312  55 kellekakeekkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceele 109
                                                             +++l +ak++ ++i +i++sGQ+HglvlLD++gkvlr a+LW+Dt+t+ e+++l 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037  63 RRALLAAKTNGQSILGIGVSGQQHGLVLLDDQGKVLRAAKLWCDTETTPENDRLL 117
                                                             ******************************************************* PP

                                               TIGR01312 110 eelg.eeelleltgnlalegfTapKllWvrkhepevfariakvlLPkDylrykLt 163
                                                             ++lg e+ +l+++g ++++g+T++KllW+++++pevf ri+ +lLP+Dyl+++Lt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 118 AHLGgEKGSLKRLGVVIAPGYTLSKLLWTKEQHPEVFSRISRILLPHDYLNHWLT 172
                                                             ******************************************************* PP

                                               TIGR01312 164 gevvteysDAsGTllfdvkkrewskellkaldle...esllPklvessekaGkvr 215
                                                             g+ ++ey+DAsGT++f+v++r+w+ +ll+ +d++   +++lP+l+++++ +G++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 173 GRSCSEYGDASGTGYFNVRTRQWDGQLLRDIDPSgrlQAALPELIAPHQAVGTIL 227
                                                             **********************************99999**************** PP

                                               TIGR01312 216 eevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkae 270
                                                             + +a++lG++    v++Gggdn++gAiG+g++++g++++slG+SG+v+a++d+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 228 PGIAEHLGINPRALVSSGGGDNMMGAIGTGNIQPGAITMSLGSSGTVYAYADQPN 282
                                                             ******************************************************* PP

                                               TIGR01312 271 sdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvev 325
                                                             + +++av++Fc+++ g+w+pl++t+++t+a++ ++ell  ld++++n +++++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 283 VATDAAVATFCSSS-GGWLPLICTMNLTNATSLIRELLD-LDIDQFNDLVAQAPI 335
                                                             **************.***********************9.*************** PP

                                               TIGR01312 326 gaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrds 379
                                                             ga+gv++lP+++GER+P+l p+a++sl Glt +n tra+l+rAv+eg++f+lr++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 336 GADGVCMLPFFNGERVPAL-PHASASLSGLTmTNLTRANLCRAVVEGTTFGLRYG 389
                                                             *******************.***********8999******************** PP

                                               TIGR01312 380 ldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAil 434
                                                             ld+l++ +gl++++irliGGG+ks+vwrqi+ad ++++v ++e++e+aalGaAi+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 390 LDLLRR-NGLQSRSIRLIGGGSKSAVWRQIVADTMNTPVICTEQSEAAALGAAIQ 443
                                                             ******.88********************************************** PP

                                               TIGR01312 435 Aaialg.....ekdlveecseavvkqkes.vepiaenveayeelyerykkly 480
                                                             Aa++ +     e++l+++c+++v+ + +s + p+a nv+a +++yery++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3037 444 AAWCVSranghEDSLAQLCERCVKLDPASeTLPVADNVQACQQAYERYQQHV 495
                                                             ****98777777778999******999999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (498 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: 11.08
//
[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