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 3608572 Dshi_1966 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Dino:3608572
          Length = 580

 Score =  691 bits (1783), Expect = 0.0
 Identities = 356/591 (60%), Positives = 433/591 (73%), Gaps = 14/591 (2%)

Query: 4   IEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKV 63
           +++KVPDIGDF  V V+ +LV  GDTV  E  LI LESDKA+M+VPS AAG V E+KV  
Sbjct: 1   MDIKVPDIGDFTDVPVVSILVAVGDTVAEEDPLIELESDKATMEVPSPAAGVVKEIKVAE 60

Query: 64  GDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCEM 123
           GD V +G VI   E+  A  AP  A      +APA AAAAP    A  + +G  D+  E+
Sbjct: 61  GDNVSEGTVIMVFESSGAEEAPKGAD-----EAPA-AAAAPEAVAATGTATGPGDVHGEV 114

Query: 124 LVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKAL 183
           +VLG+GPGGY+AAFRAADLG   VL+ERY +LGGVCLNVGCIPSKALLH A VI EA+ +
Sbjct: 115 VVLGSGPGGYTAAFRAADLGKKVVLIERYPSLGGVCLNVGCIPSKALLHVAKVITEAEEM 174

Query: 184 AAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVEL 243
            AHG+ FG+ K+DLD LR +K+ V+G+LTGGL+G+AK RKV+VV G G F  P+ + VE 
Sbjct: 175 GAHGVSFGKPKVDLDELRAFKDSVIGQLTGGLSGLAKGRKVEVVTGYGKFTGPNMIAVEG 234

Query: 244 TEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLVIG 303
            +G         T + F++ IIAAGS+ V LPF+PED RI+DSTGALEL ++P +ML++G
Sbjct: 235 EDGV--------TTVSFDQCIIAAGSEPVNLPFLPEDDRIIDSTGALELKDIPKRMLILG 286

Query: 304 GGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTVGV 363
           GGIIGLEMA VY  LG+DI VVE +D LM GAD+D+VK   K+ + R+  ++LKTK  GV
Sbjct: 287 GGIIGLEMACVYDALGSDITVVEFMDQLMPGADKDIVKPLHKRIEGRYENILLKTKVTGV 346

Query: 364 EAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDKQM 423
           EA   G+ V FE          +D VLV+VGR PNG  I AEKAGVAV ERGFI VD Q 
Sbjct: 347 EALKKGLKVTFEDAKGELTTDTFDKVLVAVGRKPNGALIDAEKAGVAVDERGFIAVDSQQ 406

Query: 424 RTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAG 483
           RT V HIFAIGD+VGQPMLAHKAVHE  VAAE   G   +FDA+ IPSVA+TDPEVAW G
Sbjct: 407 RTGVAHIFAIGDLVGQPMLAHKAVHEGKVAAEVCAGHNRHFDARLIPSVAYTDPEVAWCG 466

Query: 484 LTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAGDL 543
           +TE + K KGI Y KGVFPWAASGR+++NGR EG TKL+FD E  RVIG  IVGT+AGDL
Sbjct: 467 VTETDAKAKGIAYEKGVFPWAASGRSLSNGRSEGITKLLFDPEDDRVIGACIVGTNAGDL 526

Query: 544 ISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           ISEV LAIEMGADAVD+G TIHPHPTL E++  AAE++EGT TD+ PP+K+
Sbjct: 527 ISEVALAIEMGADAVDLGHTIHPHPTLSETVNFAAEMFEGTITDLMPPKKK 577


Lambda     K      H
   0.316    0.134    0.387 

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: 988
Number of extensions: 52
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: 594
Length of database: 580
Length adjustment: 37
Effective length of query: 557
Effective length of database: 543
Effective search space:   302451
Effective search space used:   302451
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate 3608572 Dshi_1966 (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.15550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.1e-153  497.2   0.9   2.7e-153  496.9   0.9    1.1  1  lcl|FitnessBrowser__Dino:3608572  Dshi_1966 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608572  Dshi_1966 dihydrolipoamide dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.9   0.9  2.7e-153  2.7e-153       3     455 ..     113     565 ..     111     570 .. 0.96

  Alignments for each domain:
  == domain 1  score: 496.9 bits;  conditional E-value: 2.7e-153
                         TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldle 78 
                                       +vvv+G+GpgGY+aA raa lg+kv+l+e+  +lGG+ClnvGCiP+KalL+ a+v++e++e+  +g++  + k+dl+
  lcl|FitnessBrowser__Dino:3608572 113 EVVVLGSGPGGYTAAFRAADLGKKVVLIERyPSLGGVCLNVGCIPSKALLHVAKVITEAEEMGAHGVSFGKPKVDLD 189
                                       79****************************99********************************************* PP

                         TIGR01350  79 kllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleedek 155
                                       +l + k++v+ +l+gG+++L k  kvev++G++k+++++ + v++e++ ++++++++iiA Gsep +lp+ l ed  
  lcl|FitnessBrowser__Dino:3608572 190 ELRAFKDSVIGQLTGGLSGLAKGRKVEVVTGYGKFTGPNMIAVEGEDGVTTVSFDQCIIAAGSEPVNLPF-LPEDD- 264
                                       ***********************************************99*********************.66665. PP

                         TIGR01350 156 vvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltna 232
                                       ++i+s++alelk +p++++i+GgG+iG+E+a+++  lG+++tv+e++d+++p  d+++ k l+k+++ +  +il ++
  lcl|FitnessBrowser__Dino:3608572 265 RIIDSTGALELKDIPKRMLILGGGIIGLEMACVYDALGSDITVVEFMDQLMPGADKDIVKPLHKRIEGRYENILLKT 341
                                       6**************************************************************************** PP

                         TIGR01350 233 kvtevekeedevv..veakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGD 307
                                       kvt ve+ ++ ++  +e  k+e +t + +kvLvavGrkpn   ++ ek gv +derg+i vd++ rt v++i+aiGD
  lcl|FitnessBrowser__Dino:3608572 342 KVTGVEALKKGLKvtFEDAKGELTTDTFDKVLVAVGRKPNGALIDAEKAGVAVDERGFIAVDSQQRTGVAHIFAIGD 418
                                       ***888777766622666666999999************************************************** PP

                         TIGR01350 308 vigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkala 384
                                       ++g++mLAh+A++eg vaae  ag+++ ++d++++Psv yt+Peva  G+te++ak++gi+++ g fp aa+g++l+
  lcl|FitnessBrowser__Dino:3608572 419 LVGQPMLAHKAVHEGKVAAEVCAGHNR-HFDARLIPSVAYTDPEVAWCGVTETDAKAKGIAYEKGVFPWAASGRSLS 494
                                       ************************776.9************************************************ PP

                         TIGR01350 385 leetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaal 455
                                        + ++G+ k+++d+++++++Ga+ivg++a +lise+ala+e+++ + +l +tihpHPtlsE+++ aa+   
  lcl|FitnessBrowser__Dino:3608572 495 NGRSEGITKLLFDPEDDRVIGACIVGTNAGDLISEVALAIEMGADAVDLGHTIHPHPTLSETVNFAAEMFE 565
                                       ***************************************************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (580 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: 9.65
//
[ok]

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

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Protein sequences (fasta format)
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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