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.6698.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: 11.47
//
[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:

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:

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:

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:

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