Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2E3

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate AO353_25905 AO353_25905 xylulose kinase

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



>FitnessBrowser__pseudo3_N2E3:AO353_25905
          Length = 497

 Score =  805 bits (2080), Expect = 0.0
 Identities = 400/497 (80%), Positives = 437/497 (87%), Gaps = 2/497 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           M+ + LFLGIDCGTQGTKALILD+ SG+VLG GAAAHS+IS ANGRREQD  QWL+A T 
Sbjct: 1   MSIRNLFLGIDCGTQGTKALILDSRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTL 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           AT QAL AA + G+ ILGIGVSGQQHGLVLLD+QGQVLRPAKLWCDTETT EN RLLAHL
Sbjct: 61  ATRQALLAANISGREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSLERLGV IAPGYTVSKLLWT EQHPQ+F RIA +LLPHD+LNYWLTGR CSE+G
Sbjct: 121 GGESGSLERLGVAIAPGYTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVR+RQWD+QLL+ IDPS RLQAALPEL+EAHQ VG ILP IA  LGINP+A
Sbjct: 181 DASGTGYFNVRSRQWDLQLLRDIDPSGRLQAALPELLEAHQAVGTILPDIAERLGINPKA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           +VASGGGDNMMGA+GTGNIQPG ITMSLGSSGTVYAYA +P VSP  +VATFCSSSGGWL
Sbjct: 241 LVASGGGDNMMGALGTGNIQPGAITMSLGSSGTVYAYAEQPNVSPDAAVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNAT A+REL DLD+  FNA V ++PIGAEGV MLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATSAVRELFDLDLSQFNARVEQSPIGAEGVSMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           LLGL  +NLT+ANLCRAVVEGTTFGLRYGLDLLR NGLQ++SIRL GGGSKS  WRQ+VA
Sbjct: 361 LLGLNMSNLTQANLCRAVVEGTTFGLRYGLDLLRHNGLQSRSIRLTGGGSKSPAWRQMVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHS--GSQTGLAELCERCVKLDPSSETRPIAAHV 478
           D M+T V+CTE SEAAALGAAIQAAWC S  G+Q  L  LCERCV LDPSSET+P+AA+V
Sbjct: 421 DIMNTPVVCTEHSEAAALGAAIQAAWCESAAGTQQSLLALCERCVSLDPSSETQPVAANV 480

Query: 479 AASQQAYERYRQHVATL 495
           AA QQAYERYRQ VATL
Sbjct: 481 AAYQQAYERYRQQVATL 497


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: 891
Number of extensions: 31
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: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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 AO353_25905 AO353_25905 (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.23311.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   8.6e-190  617.2   0.0   9.8e-190  617.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  AO353_25905 xylulose kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  AO353_25905 xylulose kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.0   0.0  9.8e-190  9.8e-190       1     479 [.       8     493 ..       8     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 617.0 bits;  conditional E-value: 9.8e-190
                                     TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakee 64 
                                                   lGiD+gT+++Kal++d  +g+v+++g+a++++is+++g++Eqdp +wleal+ a++++l +a+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905   8 LGIDCGTQGTKALILDsRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTLATRQALLAANIS 72 
                                                   7***************99*********************************************** PP

                                     TIGR01312  65 kkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlaleg 128
                                                    +ei +i++sGQ+HglvlLDe+g+vlrpa+LW+Dt+t++e+++l ++lg e+ +le++g ++++g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  73 GREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHLGgESGSLERLGVAIAPG 137
                                                   *************************************************9*************** PP

                                     TIGR01312 129 fTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellka 193
                                                   +T++KllW+ +++p++faria++lLP+Dyl+y+Ltg+ ++e +DAsGT++f+v+ r+w+ +ll+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 138 YTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFGDASGTGYFNVRSRQWDLQLLRD 202
                                                   ***************************************************************** PP

                                     TIGR01312 194 ldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvs 255
                                                   +d++   +++lP+l+e+++ +G++ +++a++lG++ +  va+Gggdn++gA+G+g++++g++++s
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 203 IDPSgrlQAALPELLEAHQAVGTILPDIAERLGINPKALVASGGGDNMMGALGTGNIQPGAITMS 267
                                                   ****99999******************************************************** PP

                                     TIGR01312 256 lGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneea 320
                                                   lG+SG+v+a++++++++p++av++Fc+++ g+w+pl++t+++t+a++ ++el+  ld++++n+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 268 LGSSGTVYAYAEQPNVSPDAAVATFCSSS-GGWLPLICTMNLTNATSAVRELFD-LDLSQFNARV 330
                                                   *****************************.************************.********** PP

                                     TIGR01312 321 ekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrdsldilk 384
                                                   e++++gaegv++lP+l+GER+P+l p+a+gsl+Gl+ +n t+a+l+rAv+eg++f+lr++ld+l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 331 EQSPIGAEGVSMLPFLNGERVPAL-PHATGSLLGLNmSNLTQANLCRAVVEGTTFGLRYGLDLLR 394
                                                   ************************.***********8999************************* PP

                                     TIGR01312 385 elkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialg....ekdlv 445
                                                   + +gl++++irl+GGG+ks++wrq++adi++++vv++e++e+aalGaAi+Aa++++    +++l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 395 H-NGLQSRSIRLTGGGSKSPAWRQMVADIMNTPVVCTEHSEAAALGAAIQAAWCESaagtQQSLL 458
                                                   *.88**************************************************99888778899 PP

                                     TIGR01312 446 eecseavvkqkes.vepiaenveayeelyerykkl 479
                                                   ++c+++v+ + +s ++p+a+nv+ay+++yery++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 459 ALCERCVSLDPSSeTQPVAANVAAYQQAYERYRQQ 493
                                                   **********9999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (497 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 0.02s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.24
//
[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