Alignments for a candidate for lpd in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Algoriphagus machipongonensis PR1

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 WP_008198582.1 ALPR1_RS03970 dihydrolipoyl dehydrogenase

Query= SwissProt::Q9M5K3
         (507 letters)



>NCBI__GCF_000166275.1:WP_008198582.1
          Length = 466

 Score =  487 bits (1253), Expect = e-142
 Identities = 243/464 (52%), Positives = 335/464 (72%), Gaps = 2/464 (0%)

Query: 45  DVVIIGGGPGGYVAAIKASQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           DV++IG GPGGYVAAI+ +QLG+KT  +EK   LGGTCLNVGCIPSKALL SS  YH A 
Sbjct: 4   DVIVIGSGPGGYVAAIRCAQLGMKTAIVEKYPTLGGTCLNVGCIPSKALLDSSEHYHNAA 63

Query: 105 HSFANHGIKVSSVEVDLPAMLAQKDNAVKNLTRGIEGLFKKNKVTYVKGYGKFISPNEVS 164
           H+F  HGI +S+++VDL  M+ +K++ VK  T GI+ L KKNK+   +G G F+    V 
Sbjct: 64  HTFKTHGINLSNLKVDLKQMITRKNDVVKQNTDGIQYLMKKNKIEVHQGVGSFVDKTTVK 123

Query: 165 VETIDGGNTIVKGKHIIVATGSDVKSLPGITIDEKKIVSSTGALSLSEVPKKLIVIGAGY 224
           V   DG ++ ++GK+IIVATGS   +LP I +D+ ++++ST AL+L E PK L+VIG G 
Sbjct: 124 VTKDDGSSSDIQGKNIIVATGSKPSNLPFIKLDKDRVITSTEALNLKETPKHLVVIGGGV 183

Query: 225 IGLEMGSVWGRLGSEVTVVEFAGDIVPSMDGEIRKQFQRSLEKQKMKFMLKTKVVSVDSS 284
           IGLE+GSV+ RLG++V+V+EF   ++P+MD  + K+ Q+SL+K   +F LK KV +V+  
Sbjct: 184 IGLELGSVYARLGAKVSVIEFMDSLIPTMDRTMGKELQKSLKKIGFEFFLKHKVTAVEKK 243

Query: 285 SDGVKLTVEPAEGGEQSILEADVVLVSAGRTPFTSGLDLEKIGVETDKAGRILVNDRFLS 344
              V +  + A+ GE   ++ D VLVS GR P+T GL+ E  G++    G+I VND   +
Sbjct: 244 GKEVTVKADNAK-GETVEIKGDYVLVSIGRRPYTDGLNAEAAGLKLTDRGQIEVNDHLQT 302

Query: 345 NVPGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTHPEVASVGKT 404
           NVP +YAIGDV+ G MLAHKAEE+GV   E + G+  H++Y+ +PGVVYT PEVA+VG T
Sbjct: 303 NVPNIYAIGDVVKGAMLAHKAEEEGVFVAETLVGQKPHINYNLIPGVVYTWPEVAAVGYT 362

Query: 405 EEQLKKEGVSYRVGKFPFMANSRAKAIDNAEGLVKILADKETDKILGVHIMAPNAGELIH 464
           EEQLK++G+ Y+ GKFPFMA+ RA+A  + +GLVK+LAD ETD+ILGVH++ P   ++I 
Sbjct: 363 EEQLKEKGIKYKAGKFPFMASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIA 422

Query: 465 EAVLAINYDASSEDIARVCHAHPTMSEALKEAAMATYD-KPIHI 507
           EAV+A+ Y AS+EDIAR+ HAHPT +EA KEA +A  D + +HI
Sbjct: 423 EAVVAMEYRASAEDIARMSHAHPTYTEAFKEACLAATDNRALHI 466


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: 616
Number of extensions: 20
Number of successful extensions: 2
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: 466
Length adjustment: 34
Effective length of query: 473
Effective length of database: 432
Effective search space:   204336
Effective search space used:   204336
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 WP_008198582.1 ALPR1_RS03970 (dihydrolipoyl dehydrogenase)
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.3521721.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-185  601.6   9.9   5.3e-185  601.4   9.9    1.0  1  NCBI__GCF_000166275.1:WP_008198582.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166275.1:WP_008198582.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.4   9.9  5.3e-185  5.3e-185       1     457 [.       2     461 ..       2     466 .] 0.98

  Alignments for each domain:
  == domain 1  score: 601.4 bits;  conditional E-value: 5.3e-185
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieve 71 
                                           +ydv+viG+GpgGYvaAir+aqlg+k+a+vek  +lGGtClnvGCiP+KalL s+e ++++ + +k++gi+++
  NCBI__GCF_000166275.1:WP_008198582.1   2 NYDVIVIGSGPGGYVAAIRCAQLGMKTAIVEKyPTLGGTCLNVGCIPSKALLDSSEHYHNAAHtFKTHGINLS 74 
                                           69******************************99*************************************** PP

                             TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsep 143
                                           n+k+dl+++  rk+ vvk+ ++G+++L+kknk+ev++G ++++dk++v+v+k++++ + ++ knii+AtGs+p
  NCBI__GCF_000166275.1:WP_008198582.1  75 NLKVDLKQMITRKNDVVKQNTDGIQYLMKKNKIEVHQGVGSFVDKTTVKVTKDDGSsSDIQGKNIIVATGSKP 147
                                           ****************************************************9988799************** PP

                             TIGR01350 144 relplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskv 216
                                           ++lp+ ++ d+++vits+eal+lke+p++lv++GgGviG+E++s++a+lG+kv+vie++d ++p++d+++ k+
  NCBI__GCF_000166275.1:WP_008198582.1 148 SNLPF-IKLDKDRVITSTEALNLKETPKHLVVIGGGVIGLELGSVYARLGAKVSVIEFMDSLIPTMDRTMGKE 219
                                           *****.8888888************************************************************ PP

                             TIGR01350 217 lkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnleelgleklgvelderg 287
                                           l+k+lkk g ++  ++kvt+vek+ +ev+v+a++   e+ ++++++vLv++Gr+p +++l+ e+ g++l++rg
  NCBI__GCF_000166275.1:WP_008198582.1 220 LQKSLKKIGFEFFLKHKVTAVEKKGKEVTVKADNAkgETVEIKGDYVLVSIGRRPYTDGLNAEAAGLKLTDRG 292
                                           *****************************8776654589999******************************* PP

                             TIGR01350 288 aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGltee 360
                                           +i+v+++l+tnvp+iyaiGDv++++mLAh+A++egv +ae+++g+++ +i+y+++P v+yt Peva+vG+tee
  NCBI__GCF_000166275.1:WP_008198582.1 293 QIEVNDHLQTNVPNIYAIGDVVKGAMLAHKAEEEGVFVAETLVGQKP-HINYNLIPGVVYTWPEVAAVGYTEE 364
                                           ********************************************998.9************************ PP

                             TIGR01350 361 qakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveel 433
                                           q+ke+gi++k+gkfpf+a+g+a+a+ +tdG+vkv++d +t+eilG+h++g++ +++i+e+++a+e ++++e++
  NCBI__GCF_000166275.1:WP_008198582.1 365 QLKEKGIKYKAGKFPFMASGRARASMDTDGLVKVLADAETDEILGVHMIGPRTADMIAEAVVAMEYRASAEDI 437
                                           ************************************************************************* PP

                             TIGR01350 434 aktihpHPtlsEaikeaalaalgk 457
                                           a++ h+HPt++Ea+kea+laa+++
  NCBI__GCF_000166275.1:WP_008198582.1 438 ARMSHAHPTYTEAFKEACLAATDN 461
                                           *******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.97
//
[ok]

This GapMind analysis is from Sep 24 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