Alignments for a candidate for lpd in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Dinoroseobacter shibae DFL-12

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 3608411 Dshi_1811 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Dino:3608411
          Length = 465

 Score =  538 bits (1385), Expect = e-157
 Identities = 264/462 (57%), Positives = 345/462 (74%), Gaps = 2/462 (0%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD++V+G GPGGYVAAIRAAQL LKVA+VER H+GGICLNWGCIPTK++LRS+EV+H M 
Sbjct: 6   FDMVVVGAGPGGYVAAIRAAQLGLKVAIVEREHMGGICLNWGCIPTKAMLRSSEVFHLMH 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
            A+ +GL +    +DLD ++ARSR +A +L SGV  L++KNKV V+ G   L     + V
Sbjct: 66  RAKEFGLKADGVGYDLDAVVARSRAIAKQLNSGVSHLMKKNKVTVVMGEASLPAKGTVAV 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           +T +G E  L A  +++ATGARAR+LP + +DG  +WTY HAL P  MPKKLLVIGSGAI
Sbjct: 126 KTDKGTET-LRAPHVVLATGARARELPGLEADGDLVWTYKHALTPKRMPKKLLVIGSGAI 184

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPDD 244
           GIEFASFY   G E ++VE   +ILP+EDAE+S +  K F+K+G+ I  ++ +++L    
Sbjct: 185 GIEFASFYNTLGTETTVVEVMDRILPVEDAEISGFAKKQFEKQGMTIREKAMVKSLERGK 244

Query: 245 EGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNVD 304
             VTA+I    GK T E F   I A+G+V N E +GL+ LG+++++  +  D + RT V+
Sbjct: 245 GTVTAQIEQG-GKTTAETFDTVISAVGIVGNTEKLGLEALGVRVEKTHVVTDAYCRTGVE 303

Query: 305 HVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLTE 364
            ++AIGD+AGAP LAHKASH+GV+ AE IAG + VHP+   +I GCTY +PQ+ASVG+TE
Sbjct: 304 GLYAIGDLAGAPWLAHKASHEGVMVAELIAGRNDVHPVTPDSIAGCTYCQPQIASVGMTE 363

Query: 365 EKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQG 424
            +A++ G+ +K+G FPFI NGKAIA G  +G +KTVFDA +G LLGAHMVGAEVTE+IQG
Sbjct: 364 AQAKEAGHKIKVGRFPFIGNGKAIALGEPEGMIKTVFDAGTGELLGAHMVGAEVTELIQG 423

Query: 425 YTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           Y V R LETTE ++M T+FPHPTLSE MHESVL AYGRALHF
Sbjct: 424 YVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAYGRALHF 465


Lambda     K      H
   0.319    0.135    0.393 

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: 677
Number of extensions: 26
Number of successful extensions: 4
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 3608411 Dshi_1811 (dihydrolipoamide dehydrogenase (RefSeq))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

# 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/TIGR01350.hmm
# target sequence database:        /tmp/gapView.22170.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01350  [M=461]
Accession:   TIGR01350
Description: lipoamide_DH: dihydrolipoyl dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.6e-171  557.0   7.2   1.8e-171  556.8   7.2    1.0  1  lcl|FitnessBrowser__Dino:3608411  Dshi_1811 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608411  Dshi_1811 dihydrolipoamide dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  556.8   7.2  1.8e-171  1.8e-171       2     461 .]       6     465 .]       5     465 .] 0.99

  Alignments for each domain:
  == domain 1  score: 556.8 bits;  conditional E-value: 1.8e-171
                         TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldle 78 
                                       +d+vv+G+GpgGYvaAiraaqlglkva+ve+e++GG+Cln+GCiPtKa+L+s+ev++ ++ ake+g+++++v +dl+
  lcl|FitnessBrowser__Dino:3608411   6 FDMVVVGAGPGGYVAAIRAAQLGLKVAIVEREHMGGICLNWGCIPTKAMLRSSEVFHLMHRAKEFGLKADGVGYDLD 82 
                                       8********************************************************9999**************** PP

                         TIGR01350  79 kllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedek 155
                                       ++++r++++ k+l++Gv++L+kknkv+v++Gea+l  k++v vk++k++++l+a ++++AtG++ relp+ le+d++
  lcl|FitnessBrowser__Dino:3608411  83 AVVARSRAIAKQLNSGVSHLMKKNKVTVVMGEASLPAKGTVAVKTDKGTETLRAPHVVLATGARARELPG-LEADGD 158
                                       **********************************************************************.****** PP

                         TIGR01350 156 vvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltna 232
                                       +v+t+++al+ k++p++l+++G+G+iG+Efas++++lG++ tv+e++drilp++dae+s ++kk+++k+g++i ++a
  lcl|FitnessBrowser__Dino:3608411 159 LVWTYKHALTPKRMPKKLLVIGSGAIGIEFASFYNTLGTETTVVEVMDRILPVEDAEISGFAKKQFEKQGMTIREKA 235
                                       ***************************************************************************** PP

                         TIGR01350 233 kvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDv 308
                                       +v+++e+ + +v+++++++ +++  + + v+ avG   n+e+lgle+lgv++++   +++d+++rt v+g+yaiGD+
  lcl|FitnessBrowser__Dino:3608411 236 MVKSLERGKGTVTAQIEQGgKTTAETFDTVISAVGIVGNTEKLGLEALGVRVEK-THVVTDAYCRTGVEGLYAIGDL 311
                                       *************999888789999***************************99.77******************** PP

                         TIGR01350 309 igklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkala 384
                                       +g + LAh+As+egv++ae iag+++   +  + +  ++y++P++asvG+te+qake+g+++kvg+fpf  ngka+a
  lcl|FitnessBrowser__Dino:3608411 312 AGAPWLAHKASHEGVMVAELIAGRNDVhPVTPDSIAGCTYCQPQIASVGMTEAQAKEAGHKIKVGRFPFIGNGKAIA 388
                                       ***********************9998799*********************************************** PP

                         TIGR01350 385 leetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                       l+e +G++k+++d  tge+lGah+vgae++eli+  ++  +le+t+e+l++t++pHPtlsE+++e++l+a+g+a+h+
  lcl|FitnessBrowser__Dino:3608411 389 LGEPEGMIKTVFDAGTGELLGAHMVGAEVTELIQGYVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAYGRALHF 465
                                       *************************************************************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 00:00:00.02
# Mc/sec: 7.59
//
[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