Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N1B4

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate Pf1N1B4_4845 Xylulose kinase (EC 2.7.1.17)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845
          Length = 498

 Score =  847 bits (2188), Expect = 0.0
 Identities = 424/498 (85%), Positives = 452/498 (90%), Gaps = 3/498 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           MANQQLFLGIDCGTQGTKA+ILD  SGQVLGQGAAAHS+ISGANGRREQDT QWL+AFTQ
Sbjct: 1   MANQQLFLGIDCGTQGTKAVILDAQSGQVLGQGAAAHSLISGANGRREQDTAQWLEAFTQ 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYL 120
           AT +AL AA VDGQAILGIGVSGQQHGLVLLDD+GQ LRPAKLWCDTE+T ENDRLLA+L
Sbjct: 61  ATRRALLAANVDGQAILGIGVSGQQHGLVLLDDRGQALRPAKLWCDTESTLENDRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSLERLGVVIAPGYTVSKLLWT+EQHPQVF RIA +LLPHD+LNYWLTGR CSEYG
Sbjct: 121 GGEKGSLERLGVVIAPGYTVSKLLWTKEQHPQVFARIARILLPHDYLNYWLTGRSCSEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDA 240
           DASGTGYFNVRTRQWD+QLL+ IDP+ RLQAALPELI+AHQPVG ILP+IA HLGINP A
Sbjct: 181 DASGTGYFNVRTRQWDLQLLRDIDPTGRLQAALPELIDAHQPVGTILPSIAEHLGINPHA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWL 300
           +V+SGGGDNMMGAIGTGNI+PG ITMSLGSSGTVYAYA +  VSP  SVATFCSS+GGWL
Sbjct: 241 LVSSGGGDNMMGAIGTGNIKPGAITMSLGSSGTVYAYAEQANVSPDASVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATAS 360
           PLICTMNLTNATGAIREL +LDI+AFNALV QAPIGA GVCMLPFLNGERVPALPHA  S
Sbjct: 301 PLICTMNLTNATGAIRELFELDIEAFNALVAQAPIGAGGVCMLPFLNGERVPALPHAGGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVA 420
           LLGLT TNLTRANLCRAVVEGTTFGLRYGLDLLR NGL++  I LIGGGSKSPVWRQIVA
Sbjct: 361 LLGLTMTNLTRANLCRAVVEGTTFGLRYGLDLLRQNGLQSLRICLIGGGSKSPVWRQIVA 420

Query: 421 DIMDTTVICTEQSEAAALGAAIQAAWCHS---GAQDSLAELCERCVKLDPASETRPVTAH 477
           DIM+T VICTEQSEAAALGAAIQAAWC S   G +DSLA LCERCVKLD ASET P+  +
Sbjct: 421 DIMNTPVICTEQSEAAALGAAIQAAWCKSWANGQEDSLAALCERCVKLDLASETLPIAEN 480

Query: 478 VTASQQAYERYRQHVATL 495
           V A QQAYERYRQHVATL
Sbjct: 481 VAACQQAYERYRQHVATL 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: 951
Number of extensions: 37
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 Pf1N1B4_4845 (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.24692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   9.6e-187  607.2   0.0   1.1e-186  607.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845  Xylulose kinase (EC 2.7.1.17)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845  Xylulose kinase (EC 2.7.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.0   0.0  1.1e-186  1.1e-186       1     480 [.       8     495 ..       8     496 .. 0.98

  Alignments for each domain:
  == domain 1  score: 607.0 bits;  conditional E-value: 1.1e-186
                                      TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekake 63 
                                                    lGiD+gT+++Ka+++d ++g+v+++g+a++++is ++g++Eqd+ +wlea+++a++++l +a++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845   8 LGIDCGTQGTKAVILDaQSGQVLGQGAAAHSLISGANGRREQDTAQWLEAFTQATRRALLAANV 71 
                                                    7***************99********************************************** PP

                                      TIGR01312  64 ekkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlal 126
                                                    + ++i +i++sGQ+HglvlLD+ g++lrpa+LW+Dt+++ e+++l ++lg e+ +le++g +++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845  72 DGQAILGIGVSGQQHGLVLLDDRGQALRPAKLWCDTESTLENDRLLAHLGgEKGSLERLGVVIA 135
                                                    **************************************************************** PP

                                      TIGR01312 127 egfTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskel 190
                                                    +g+T++KllW+++++p+vfaria +lLP+Dyl+y+Ltg+ ++ey+DAsGT++f+v++r+w+ +l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 136 PGYTVSKLLWTKEQHPQVFARIARILLPHDYLNYWLTGRSCSEYGDASGTGYFNVRTRQWDLQL 199
                                                    **************************************************************** PP

                                      TIGR01312 191 lkaldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegk 251
                                                    l+ +d+    +++lP+l+++++ +G++ +++a++lG++ +  v++Gggdn++gAiG+g++k+g+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 200 LRDIDPTgrlQAALPELIDAHQPVGTILPSIAEHLGINPHALVSSGGGDNMMGAIGTGNIKPGA 263
                                                    ******999999**************************************************** PP

                                      TIGR01312 252 vlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldvee 315
                                                    +++slG+SG+v+a++++a+++p+++v++Fc+++ g+w+pl++t+++t+a+  ++el++ ld+e+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 264 ITMSLGSSGTVYAYAEQANVSPDASVATFCSSS-GGWLPLICTMNLTNATGAIRELFE-LDIEA 325
                                                    *********************************.************************.***** PP

                                      TIGR01312 316 lneeaekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrd 378
                                                    +n++++++++ga gv++lP+l+GER+P+l p+a gsl+Glt +n tra+l+rAv+eg++f+lr+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 326 FNALVAQAPIGAGGVCMLPFLNGERVPAL-PHAGGSLLGLTmTNLTRANLCRAVVEGTTFGLRY 388
                                                    *****************************.***********8999******************* PP

                                      TIGR01312 379 sldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialg.. 440
                                                    +ld+l++ +gl++ +i liGGG+ks+vwrqi+adi++++v ++e++e+aalGaAi+Aa++++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 389 GLDLLRQ-NGLQSLRICLIGGGSKSPVWRQIVADIMNTPVICTEQSEAAALGAAIQAAWCKSwa 451
                                                    *******.88**************************************************9866 PP

                                      TIGR01312 441 ...ekdlveecseavvkqkes.vepiaenveayeelyerykkly 480
                                                       e++l+++c+++v+ + +s + piaenv+a +++yery++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4845 452 ngqEDSLAALCERCVKLDLASeTLPIAENVAACQQAYERYRQHV 495
                                                    6666678999*****9999988*******************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: 9.61
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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