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 1, mitochondrial; AtmLPD1; mtLPD1; Dihydrolipoamide dehydrogenase 1; Glycine cleavage system L protein 1; Pyruvate dehydrogenase complex E3 subunit 1; E3-1; PDC-E3 1; EC 1.8.1.4 (characterized)
to candidate 3609502 Dshi_2886 dihydrolipoamide dehydrogenase (RefSeq)

Query= SwissProt::Q9M5K3
         (507 letters)



>FitnessBrowser__Dino:3609502
          Length = 464

 Score =  523 bits (1348), Expect = e-153
 Identities = 259/464 (55%), Positives = 340/464 (73%), Gaps = 7/464 (1%)

Query: 45  DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           DV+IIG GPGGYV AI+ +QLGLKT C+E R  LGGTCLNVGCIPSKALLH+SH  HEA+
Sbjct: 5   DVIIIGSGPGGYVGAIRCAQLGLKTACVEGRDTLGGTCLNVGCIPSKALLHASHQVHEAE 64

Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164
           H+F   GIKV + ++D   MLA KD+ +   T+GIE LFKKNKV ++KG+       +V 
Sbjct: 65  HNFEKMGIKVPAPKIDWKTMLAYKDDVIGQNTKGIEFLFKKNKVDWLKGWASIPEAGKVK 124

Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPG--ITIDEKKIVSSTGALSLSEVPKKLIVIGA 222
           V     G+   + KHII+A+GS+  S+PG  + IDEK +V+STGAL L ++PK+++V+G 
Sbjct: 125 V-----GDETHEAKHIIIASGSEPASIPGAEVEIDEKVVVTSTGALELGKIPKRMVVVGG 179

Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVD 282
           G IGLE+GSV+ RLG+EV+V+EF   I P  D E+ +QFQ+ L KQ +KF+    V  V 
Sbjct: 180 GVIGLELGSVYARLGTEVSVIEFMDGITPGQDLEVARQFQKILTKQGLKFITGAAVQKVA 239

Query: 283 SSSDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRF 342
           ++    K+T +  +   +  LEAD+VLVS GR PFT GL L+ +GV+  + G+I  +  +
Sbjct: 240 ATKSKAKVTYKMRKDDSEDSLEADIVLVSTGRKPFTEGLGLDALGVKMTERGQIATDGSY 299

Query: 343 LSNVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVG 402
            +NVPGVYAIGDVI GPMLAHKAE++G+A  E IAG+H HV+Y  +PGV+YTHPEVASVG
Sbjct: 300 RTNVPGVYAIGDVIEGPMLAHKAEDEGMAVAEMIAGQHPHVNYGVIPGVIYTHPEVASVG 359

Query: 403 KTEEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGEL 462
           KTEEQLK EGV+Y+VGKF FM N RAKA   A+G VK+LADK TD+ILG H++ P AG+L
Sbjct: 360 KTEEQLKAEGVAYKVGKFSFMGNGRAKANFAADGFVKLLADKATDRILGAHVIGPMAGDL 419

Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEALKEAAMATYDKPIH 506
           IHE  +A+ + A++ED+AR CHAHPT SEA++EAA+A  D  IH
Sbjct: 420 IHEVCVAMEFGAAAEDLARTCHAHPTYSEAMREAALACGDGAIH 463


Lambda     K      H
   0.315    0.133    0.375 

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: 725
Number of extensions: 28
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: 507
Length of database: 464
Length adjustment: 34
Effective length of query: 473
Effective length of database: 430
Effective search space:   203390
Effective search space used:   203390
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate 3609502 Dshi_2886 (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.14500.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-177  576.4   8.8   2.3e-177  576.2   8.8    1.0  1  lcl|FitnessBrowser__Dino:3609502  Dshi_2886 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609502  Dshi_2886 dihydrolipoamide dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.2   8.8  2.3e-177  2.3e-177       1     460 [.       3     463 ..       3     464 .] 0.98

  Alignments for each domain:
  == domain 1  score: 576.2 bits;  conditional E-value: 2.3e-177
                         TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgievenvkl 75 
                                       +ydv++iG+GpgGYv Air+aqlglk+a+ve  ++lGGtClnvGCiP+KalL++++ v+e+++ ++++gi+v   k+
  lcl|FitnessBrowser__Dino:3609502   3 SYDVIIIGSGPGGYVGAIRCAQLGLKTACVEGrDTLGGTCLNVGCIPSKALLHASHQVHEAEHnFEKMGIKVPAPKI 79 
                                       59*****************************879******************************************* PP

                         TIGR01350  76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplk.le 151
                                       d++++l+ k+ v+ + ++G+++L+kknkv+ +kG a++ ++++v+v +e++    eak+iiiA+Gsep+++p++ +e
  lcl|FitnessBrowser__Dino:3609502  80 DWKTMLAYKDDVIGQNTKGIEFLFKKNKVDWLKGWASIPEAGKVKVGDETH----EAKHIIIASGSEPASIPGAeVE 152
                                       ***********************************************9985....6*****************99** PP

                         TIGR01350 152 edekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvki 228
                                        dekvv+ts++alel ++p+++v+vGgGviG+E++s++a+lG++v+vie++d i p  d ev+++ +k l+k+g+k+
  lcl|FitnessBrowser__Dino:3609502 153 IDEKVVVTSTGALELGKIPKRMVVVGGGVIGLELGSVYARLGTEVSVIEFMDGITPGQDLEVARQFQKILTKQGLKF 229
                                       ***************************************************************************** PP

                         TIGR01350 229 ltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgi 302
                                       +t+a v+  + +k++++v+++++k+  +++lea+ vLv+ Grkp +e+lgl++lgv+++erg+i +d ++rtnvpg+
  lcl|FitnessBrowser__Dino:3609502 230 ITGAAVQkvAATKSKAKVTYKMRKDdSEDSLEADIVLVSTGRKPFTEGLGLDALGVKMTERGQIATDGSYRTNVPGV 306
                                       *******5445677788889988887789************************************************ PP

                         TIGR01350 303 yaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaan 379
                                       yaiGDvi+++mLAh+A++eg+ +ae iag+++ +++y ++P viyt+PevasvG+teeq+k+eg+++kvgkf+f+ n
  lcl|FitnessBrowser__Dino:3609502 307 YAIGDVIEGPMLAHKAEDEGMAVAEMIAGQHP-HVNYGVIPGVIYTHPEVASVGKTEEQLKAEGVAYKVGKFSFMGN 382
                                       *****************************999.9******************************************* PP

                         TIGR01350 380 gkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                       g+a a   +dGfvk+++dk t++ilGah++g+ a +li+e+ +a+e+++ +e+la+t+h+HPt+sEa+ eaala  +
  lcl|FitnessBrowser__Dino:3609502 383 GRAKANFAADGFVKLLADKATDRILGAHVIGPMAGDLIHEVCVAMEFGAAAEDLARTCHAHPTYSEAMREAALACGD 459
                                       **************************************************************************999 PP

                         TIGR01350 457 kaih 460
                                        aih
  lcl|FitnessBrowser__Dino:3609502 460 GAIH 463
                                       9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (464 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: 11.49
//
[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