GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Caldicellulosiruptor kronotskyensis 2002

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_041741979.1 CALKRO_RS09060 mannonate dehydratase

Query= metacyc::MONOMER-17955
         (360 letters)



>NCBI__GCF_000166775.1:WP_041741979.1
          Length = 359

 Score =  582 bits (1499), Expect = e-171
 Identities = 263/355 (74%), Positives = 312/355 (87%)

Query: 3   LVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLKLE 62
           + FRW+G K D + LE IRQIPG+ GVV ALFDIPVGEVWP + I +LK+ VE AGLK E
Sbjct: 1   MTFRWFGPKDDNIPLEYIRQIPGIYGVVTALFDIPVGEVWPEDRIFELKKLVEGAGLKFE 60

Query: 63  VIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKKLP 122
           VIESVNVHEDIKLGLP+RDRYIENYK+TIRNLAKAGVKV+CYNFMPVFDW+RTDL KKLP
Sbjct: 61  VIESVNVHEDIKLGLPSRDRYIENYKQTIRNLAKAGVKVICYNFMPVFDWLRTDLAKKLP 120

Query: 123 DGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWDRLEKLRETFELYKNVDEEKL 182
           DGSE MEY+H +++ +TPDEL+K ++ GSQGF LPGWE  RL++L+  FE+YK+VDE KL
Sbjct: 121 DGSEVMEYNHEILKNMTPDELVKSMERGSQGFSLPGWENYRLKQLQSLFEMYKDVDENKL 180

Query: 183 FENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYNGI 242
            +NL+YFLE +IPVCE+CDVK+AIHPDDPPWS+FGLPR++TNK+NIE+ LKAVDSPYNG+
Sbjct: 181 LQNLIYFLENIIPVCEQCDVKMAIHPDDPPWSLFGLPRVVTNKKNIEKFLKAVDSPYNGL 240

Query: 243 TFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDLFE 302
           T C GSLGAN ENNIPE+IRYFGKMGRIHF HVRN+KFTGE+SFYET+H S  GS D+FE
Sbjct: 241 TLCTGSLGANRENNIPELIRYFGKMGRIHFMHVRNIKFTGERSFYETSHLSTDGSFDMFE 300

Query: 303 VMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDKMKK 357
           ++KA +DIG++GY+RPDHGR+IWGEK RPGYGLYDRALG  Y+ GLWEAIDKM +
Sbjct: 301 IIKAIYDIGFDGYLRPDHGRMIWGEKGRPGYGLYDRALGIAYLNGLWEAIDKMSR 355


Lambda     K      H
   0.322    0.142    0.448 

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: 551
Number of extensions: 20
Number of successful extensions: 1
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: 360
Length of database: 359
Length adjustment: 29
Effective length of query: 331
Effective length of database: 330
Effective search space:   109230
Effective search space used:   109230
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: 49 (23.5 bits)

Align candidate WP_041741979.1 CALKRO_RS09060 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.569895.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     6e-128  413.2   0.0   5.7e-126  406.7   0.0    2.0  1  NCBI__GCF_000166775.1:WP_041741979.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_041741979.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.7   0.0  5.7e-126  5.7e-126       3     392 ..       1     355 [.       1     357 [. 0.95

  Alignments for each domain:
  == domain 1  score: 406.7 bits;  conditional E-value: 5.7e-126
                             TIGR00695   3 qtfrwyGr.ndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 
                                           +tfrw+G+ +d + le++rq+ G+ G+vtal +ip+Gevw  + i + k+ +e aGl+++v+esv+vhe+ikl
  NCBI__GCF_000166775.1:WP_041741979.1   1 MTFRWFGPkDDNIPLEYIRQIpGIYGVVTALFDIPVGEVWPEDRIFELKKLVEGAGLKFEVIESVNVHEDIKL 73 
                                           79******7789************************************************************* PP

                             TIGR00695  74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146
                                           +   +++yienykqt+rnla+ G+kv+cynfmpv+dw rtdla++l+dGs+ + +++  ++ +       p  
  NCBI__GCF_000166775.1:WP_041741979.1  74 GLPSRDRYIENYKQTIRNLAKAGVKVICYNFMPVFDWLRTDLAKKLPDGSEVMEYNHEILKNMT------P-- 138
                                           *****************************************************99986666655......6.. PP

                             TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219
                                                 +elv+++e+ s+                lpG+e+ ++l++++ l+e+ykd+de+kl +nl +fl++i
  NCBI__GCF_000166775.1:WP_041741979.1 139 ------DELVKSMERGSQGF-------------SLPGWEN-YRLKQLQSLFEMYKDVDENKLLQNLIYFLENI 191
                                           ......9******9988765.............6******.******************************** PP

                             TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfa. 291
                                           +pv e+  vkmaihpddpp+ ++Glpr+v+ +++++k+ + +dsp ng+tlctGs+G++ +n++ el++ f+ 
  NCBI__GCF_000166775.1:WP_041741979.1 192 IPVCEQCDVKMAIHPDDPPWSLFGLPRVVTNKKNIEKFLKAVDSPYNGLTLCTGSLGANRENNIPELIRYFGk 264
                                           ***********************************************************************84 PP

                             TIGR00695 292 .driyfahlrsvkreenpktfheaahlekdv..dlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlk 361
                                            +ri+f h+r++k  ++  +f+e++hl+ d+  d++e++ka+ +       +G    + +rpdhGr +++   
  NCBI__GCF_000166775.1:WP_041741979.1 265 mGRIHFMHVRNIKFTGER-SFYETSHLSTDGsfDMFEIIKAIYDI----GFDG----Y-LRPDHGRMIWG--- 324
                                           459***********9987.9*******999844799999998665....5678....6.9**********... PP

                             TIGR00695 362 kktnpGysaigrlkGlaelrGlelalkkvaf 392
                                           +k +pGy++++r++G+a+l+Gl+ a++k+  
  NCBI__GCF_000166775.1:WP_041741979.1 325 EKGRPGYGLYDRALGIAYLNGLWEAIDKMSR 355
                                           9**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (359 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.59
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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