GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpD in Dyella japonica UNC79MFTsu3.2

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate N515DRAFT_0031 N515DRAFT_0031 2-methylcitrate dehydratase (EC 4.2.1.79)

Query= BRENDA::P74840
         (483 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0031
          Length = 483

 Score =  581 bits (1498), Expect = e-170
 Identities = 295/486 (60%), Positives = 363/486 (74%), Gaps = 6/486 (1%)

Query: 1   MSTQELNI--RPDFDREIVDIVDYVMNYEITSKVAYDTAHYCLLDTLGCGLEALEYPACK 58
           MST +L    RPD D  +VDI DYV++Y I S  AYDTA Y LLD+L   + A+++P C 
Sbjct: 1   MSTHDLRSARRPDPDPPMVDIADYVVDYRIDSAEAYDTARYMLLDSLASAMLAMKFPECV 60

Query: 59  KLLGPIVPGTVVPNGARVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLG 118
           K LGP+VPG V+P GARVPGT  +LDP QAAF IG  IRWLDFNDTWLAAEWGHPSDNLG
Sbjct: 61  KHLGPLVPGAVLPGGARVPGTSHELDPAQAAFAIGTQIRWLDFNDTWLAAEWGHPSDNLG 120

Query: 119 GILATADWLSRNAVAAGKAPLTMKQVLSGMIKAHEIQGCIALENAFNRVGLDHVLLVKVA 178
            ILA AD+L R AV  G    +++ VL   IKAHEIQGC AL N+FNRVG DHV+LV++A
Sbjct: 121 AILALADYLGRKAVREGGRASSLRDVLGWAIKAHEIQGCYALRNSFNRVGQDHVILVRLA 180

Query: 179 STAVVAEMLGLTRDEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALM 238
           STAV   MLG  +++I+ AVS +W+D  +LR+YRHAPNTG RKSWAAGDA  RAV  A+ 
Sbjct: 181 STAVATAMLGGGKEQIVTAVSHSWIDNGALRSYRHAPNTGPRKSWAAGDACRRAVIHAIN 240

Query: 239 A-KTGEMGYPSALTAKTWGFYDVSFKGETFRFQRPYGSYVMENVLFKISFPAEFHSQTAV 297
           A   G +GYPSAL+A TWG+YDV+F+G+ F F+RP+GSYVMENVLFK+S+PAEFH+QTAV
Sbjct: 241 AVDRGVVGYPSALSAATWGYYDVAFEGKAFEFERPFGSYVMENVLFKLSYPAEFHAQTAV 300

Query: 298 EAAMTLYEQMQAAGKTAADIEKVTIRTHEACLRIIDKKGPLNNPADRDHCIQYMVAVPLL 357
           E AM L+ Q+  AG+  A+I++V I T EA  RIIDK GPL N ADRDHCIQYMVAVPLL
Sbjct: 301 ECAMRLHGQV--AGR-IAEIDQVVIETQEAGARIIDKTGPLANYADRDHCIQYMVAVPLL 357

Query: 358 FGRLTAADYEDEVAQDKRIDALREKIVCYEDPAFTADYHDPEKRAIGNAITVEFTDGSRF 417
           FGRLTA DY DEVA D RIDALRE++   E+P FT DY DP++R IGN++ V F DGS  
Sbjct: 358 FGRLTADDYGDEVAADPRIDALRERMAVSENPRFTRDYFDPDRRYIGNSVQVFFKDGSHT 417

Query: 418 GEVVVEYPIGHARRRADGIPKLIEKFKINLARQFPTRQQQRILDVSLDRARLEQMPVNEY 477
            +V ++YPIGH RRRA+GIP L+ KF+  +    P  + + IL  + D A L+ MPV E+
Sbjct: 418 DKVSIDYPIGHRRRRAEGIPVLLGKFEAAIRGHLPAHRVKAILQATSDPAGLDSMPVQEF 477

Query: 478 LDLYVI 483
           L+L+ +
Sbjct: 478 LELFTL 483


Lambda     K      H
   0.321    0.136    0.408 

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: 710
Number of extensions: 25
Number of successful extensions: 3
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate N515DRAFT_0031 N515DRAFT_0031 (2-methylcitrate dehydratase (EC 4.2.1.79))
to HMM TIGR02330 (prpD: 2-methylcitrate dehydratase (EC 4.2.1.79))

# 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/TIGR02330.hmm
# target sequence database:        /tmp/gapView.28949.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02330  [M=468]
Accession:   TIGR02330
Description: prpD: 2-methylcitrate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.9e-227  740.1   0.0   5.5e-227  739.9   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031  N515DRAFT_0031 2-methylcitrate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0031  N515DRAFT_0031 2-methylcitrate dehydratase (EC 4.2.1.79)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  739.9   0.0  5.5e-227  5.5e-227       4     467 ..      18     482 ..      15     483 .] 0.99

  Alignments for each domain:
  == domain 1  score: 739.9 bits;  conditional E-value: 5.5e-227
                                    TIGR02330   4 lediadyvleyeidskeaydtaryvlldtlgcgllaleypectkllgpvvegtlvpngarvpgtsy 69 
                                                  ++diadyv++y+ids+eaydtary+lld+l   +la+++pec k+lgp+v+g + p garvpgts+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031  18 MVDIADYVVDYRIDSAEAYDTARYMLLDSLASAMLAMKFPECVKHLGPLVPGAVLPGGARVPGTSH 83 
                                                  789*************************************************************** PP

                                    TIGR02330  70 qldpvkaafnigalvrwldyndtwlaaewghpsdnlggilavadylsrkriaegkeplkvkevlea 135
                                                  +ldp +aaf ig+ +rwld+ndtwlaaewghpsdnlg+ila adyl rk++ eg    ++++vl  
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031  84 ELDPAQAAFAIGTQIRWLDFNDTWLAAEWGHPSDNLGAILALADYLGRKAVREGGRASSLRDVLGW 149
                                                  ****************************************************************** PP

                                    TIGR02330 136 mikaheiqgvlalensfnrvgldhvllvkvastavvakllgatreeilnalshafvdgqalrtyrh 201
                                                   ikaheiqg+ al nsfnrvg dhv+lv++astav++++lg+ +e+i++a+sh+++d++alr+yrh
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 150 AIKAHEIQGCYALRNSFNRVGQDHVILVRLASTAVATAMLGGGKEQIVTAVSHSWIDNGALRSYRH 215
                                                  ****************************************************************** PP

                                    TIGR02330 202 apntgsrkswaagdatsrgvrlalial.kgemgypsalsapvwgfedvlfkkeklklareygsyvm 266
                                                  apntg rkswaagda+ r+v  a+ a+ +g +gypsalsa++wg++dv f+++ ++++r++gsyvm
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 216 APNTGPRKSWAAGDACRRAVIHAINAVdRGVVGYPSALSAATWGYYDVAFEGKAFEFERPFGSYVM 281
                                                  ********************999998648************************************* PP

                                    TIGR02330 267 envlfkisfpaefhaqtaveaavklheevkerldeierivitthesairiidkkgplanpadrdhc 332
                                                  envlfk+s+paefhaqtave+a++lh +v  r++ei+++vi t+e++ riidk+gplan adrdhc
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 282 ENVLFKLSYPAEFHAQTAVECAMRLHGQVAGRIAEIDQVVIETQEAGARIIDKTGPLANYADRDHC 347
                                                  ****************************************************************** PP

                                    TIGR02330 333 lqylvavpllfgdlvaedyedavaadpridelreklevvedkrysreyleadkrsianavevffkd 398
                                                  +qy+vavpllfg+l+a+dy d+vaadprid+lre++ v e++r++r+y+++d+r i n+v+vffkd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 348 IQYMVAVPLLFGRLTADDYGDEVAADPRIDALRERMAVSENPRFTRDYFDPDRRYIGNSVQVFFKD 413
                                                  ****************************************************************** PP

                                    TIGR02330 399 gskteeveveyplghrrrrdegipklvdkfkanlatkfsskkqerilelcldqakleatpvnefld 464
                                                  gs+t++v+++yp+ghrrrr+egip+l  kf+a++  ++++++ + il+ ++d a l+++pv+efl+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 414 GSHTDKVSIDYPIGHRRRRAEGIPVLLGKFEAAIRGHLPAHRVKAILQATSDPAGLDSMPVQEFLE 479
                                                  ****************************************************************** PP

                                    TIGR02330 465 lfv 467
                                                  lf 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0031 480 LFT 482
                                                  *97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (483 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.07
//
[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