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

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.32587.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.40
//
[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