Alignments for a candidate for xylB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Halomonas desiderata SP1

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_086511125.1 BZY95_RS17220 xylulokinase

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



>NCBI__GCF_002151265.1:WP_086511125.1
          Length = 495

 Score =  563 bits (1452), Expect = e-165
 Identities = 276/488 (56%), Positives = 349/488 (71%), Gaps = 1/488 (0%)

Query: 6   LFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQATHQA 65
           +++G+DCGTQ TK +++D     +LG+ + AH +  G NGRREQ  Q+W++AF  A  +A
Sbjct: 1   MYIGVDCGTQSTKVVVVDVEGEAILGEASRAHRLSEGDNGRREQQPQEWVEAFRGAFEEA 60

Query: 66  LAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYLGGEDG 125
           +  AG++  AI  IGVSGQQHG+V LD +G  + PAKLWCDTET   N  L+A LGG  G
Sbjct: 61  VTRAGIERHAIRAIGVSGQQHGMVALDAEGLPVHPAKLWCDTETAAHNAALVARLGGAAG 120

Query: 126 SLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYGDASGT 185
            LERLG+V+  GYT SK+ W R+ +P  + RI SVLLPHD+LN+WLTG   +E GDASGT
Sbjct: 121 CLERLGLVLQTGYTASKIAWLRDTNPCAYRRIESVLLPHDYLNFWLTGEKVAEAGDASGT 180

Query: 186 GYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDAVVASG 245
           GYF+ RTR+W   +   I P       LP LI++ +P G + P +A  LG++PD VVASG
Sbjct: 181 GYFDTRTRRWRHDVFAEIAPELDPTRVLPRLIDSREPAGTLRPELARELGLSPDVVVASG 240

Query: 246 GGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWLPLICT 305
           GGDNM+GAIGTGNI PG++T+SLG+SGTV AY+ E   +    VA FC+S+GGWLPLICT
Sbjct: 241 GGDNMLGAIGTGNIAPGIVTLSLGTSGTVCAYSPESVRAESDMVANFCASHGGWLPLICT 300

Query: 306 MNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATASLLGLT 365
           MN+T+A+  +REL DLD+ AF   +  APIGAEGV +LPF NGERVP+LPHATAS LGL 
Sbjct: 301 MNVTSASTLVRELFDLDLAAFGERLAAAPIGAEGVTVLPFFNGERVPSLPHATASFLGLD 360

Query: 366 TTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVADIMDT 425
           + NLT+ANLCRAVVE  TFGLRYGL+LL      A  IRLIGGG++SPVWRQ+VAD+  T
Sbjct: 361 SRNLTQANLCRAVVESATFGLRYGLELLGPLAAGASQIRLIGGGARSPVWRQMVADVTAT 420

Query: 426 TVICTEQSEAAALGAAIQAAWCHSGAQDSLAELCERCVKLDPASETRPVTAHVTASQQAY 485
            VIC + ++AAALGAA+QAAWC       L+ELCER V LD AS   P  A V A +  Y
Sbjct: 421 PVICPQVTDAAALGAALQAAWCER-HDLPLSELCERLVHLDDASLAEPKAASVRAYETVY 479

Query: 486 ERYRQHVA 493
            RYR+ +A
Sbjct: 480 ARYREALA 487


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: 759
Number of extensions: 28
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: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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 WP_086511125.1 BZY95_RS17220 (xylulokinase)
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.3049238.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.4e-171  554.8   0.0   8.4e-171  554.6   0.0    1.0  1  NCBI__GCF_002151265.1:WP_086511125.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002151265.1:WP_086511125.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.6   0.0  8.4e-171  8.4e-171       1     479 [.       3     485 ..       3     487 .. 0.98

  Alignments for each domain:
  == domain 1  score: 554.6 bits;  conditional E-value: 8.4e-171
                             TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikais 72 
                                           +G+D+gT+s+K+++vd e + +++++s ++ +++  +g++Eq+p+ew+ea+  a++e+ ++a  e ++i+ai+
  NCBI__GCF_002151265.1:WP_086511125.1   3 IGVDCGTQSTKVVVVDvEGEAILGEASRAHRLSEGDNGRREQQPQEWVEAFRGAFEEAVTRAGIERHAIRAIG 75 
                                           7***************99999**************************************************** PP

                             TIGR01312  73 isGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlalegfTapKllWvrkhepev 144
                                           +sGQ+Hg+v+LD+eg ++ pa+LW+Dt+ta+ ++ l ++lg +  +le++g + ++g+Ta+K++W+r+ +p +
  NCBI__GCF_002151265.1:WP_086511125.1  76 VSGQQHGMVALDAEGLPVHPAKLWCDTETAAHNAALVARLGgAAGCLERLGLVLQTGYTASKIAWLRDTNPCA 148
                                           *****************************************9******************************* PP

                             TIGR01312 145 fariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldle...esllPklvessekaGkv 214
                                           ++ri++vlLP+Dyl+++Ltge+v+e +DAsGT++fd+++r+w++++++++++e   +++lP+l++s+e aG++
  NCBI__GCF_002151265.1:WP_086511125.1 149 YRRIESVLLPHDYLNFWLTGEKVAEAGDASGTGYFDTRTRRWRHDVFAEIAPEldpTRVLPRLIDSREPAGTL 221
                                           **************************************************99988899*************** PP

                             TIGR01312 215 reevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgk 287
                                           r+e+a++lGl+ +v va+Gggdn+ gAiG+g++++g+v++slGtSG+v a++ +++  ++  v++Fc +  g+
  NCBI__GCF_002151265.1:WP_086511125.1 222 RPELARELGLSPDVVVASGGGDNMLGAIGTGNIAPGIVTLSLGTSGTVCAYSPESVRAESDMVANFCASH-GG 293
                                           **********************************************************************.** PP

                             TIGR01312 288 wyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGlt.ant 359
                                           w+pl++t+++tsa   ++el+  ld++++ e  +++++gaegv++lP+++GER+P l p+a++s++Gl+  n 
  NCBI__GCF_002151265.1:WP_086511125.1 294 WLPLICTMNVTSASTLVRELFD-LDLAAFGERLAAAPIGAEGVTVLPFFNGERVPSL-PHATASFLGLDsRNL 364
                                           *********************9.**********************************.***********8899 PP

                             TIGR01312 360 tradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaA 432
                                           t+a+l+rAv+e+++f+lr++l++l  l+    ++irliGGGa+s+vwrq++ad+++++v +p+ + +aalGaA
  NCBI__GCF_002151265.1:WP_086511125.1 365 TQANLCRAVVESATFGLRYGLELLGPLA-AGASQIRLIGGGARSPVWRQMVADVTATPVICPQVTDAAALGAA 436
                                           **************************76.999***************************************** PP

                             TIGR01312 433 ilAaialg.ekdlveecseavvkqkes.vepiaenveayeelyerykkl 479
                                            +Aa+++  +  l e+c++ v+ + +s +ep+a++v+aye++y+ry++ 
  NCBI__GCF_002151265.1:WP_086511125.1 437 LQAAWCERhDLPLSELCERLVHLDDASlAEPKAASVRAYETVYARYREA 485
                                           *******97788999********99999******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (495 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: 00:00:00.00
# Mc/sec: 26.02
//
[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