Alignments for a candidate for lpd in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Magnetospirillum magneticum AMB-1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011384718.1 AMB_RS11730 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000009985.1:WP_011384718.1
          Length = 462

 Score =  543 bits (1398), Expect = e-159
 Identities = 277/464 (59%), Positives = 346/464 (74%), Gaps = 9/464 (1%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD+IV+GGGPGGYVAAIRAAQL +  ALVER HLGGICLNWGCIPTK+LLRSAE+Y  MQ
Sbjct: 6   FDIIVIGGGPGGYVAAIRAAQLGMNTALVEREHLGGICLNWGCIPTKALLRSAEIYRNMQ 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +AE+YGL++    FDL KI+ARSR V+ +L  GVK LL+KNKV VI G  +L G  ++ +
Sbjct: 66  HAESYGLSAPGATFDLAKIVARSRGVSAQLQGGVKHLLKKNKVTVIEGTAKLAGGSKVAI 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           E     +  + A  II+ATGARAR LP    DGK IWTY  AL P  MPK+LLVIGSGAI
Sbjct: 126 EG----KPTISAPHIILATGARARILPGFEPDGKFIWTYKEALVPDTMPKRLLVIGSGAI 181

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPD- 243
           GIEFASF+   GA+V++ E   ++LP+EDAE+SA   K+F+K+G++IL  + ++ L  + 
Sbjct: 182 GIEFASFFNALGAQVTVAEAMDRVLPVEDAEISAMAQKSFEKQGMKILAGANIKGLKKNA 241

Query: 244 -DEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTN 302
            D  VT E  G   +VT +R    I AIG+V NVEN+GL+    K++R  +  D + RT 
Sbjct: 242 VDVTVTIEAGGKTHEVTVDRI---ITAIGIVGNVENVGLEATKAKVERTHVITDEYCRTG 298

Query: 303 VDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGL 362
              ++AIGD+AGAP LAHKASH+ +I  E I G   VHPL+ + IPGCTY  PQVASVGL
Sbjct: 299 EPGLYAIGDIAGAPWLAHKASHEAIICVEKIKGLPDVHPLDMRKIPGCTYCHPQVASVGL 358

Query: 363 TEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMI 422
           +E KA+++GY VK+G FPF+ANGKAIA G T+G +KTVFDA +G LLGAHM+GAEVTE+I
Sbjct: 359 SEAKAKEKGYAVKVGRFPFMANGKAIALGETEGMIKTVFDAKTGELLGAHMIGAEVTELI 418

Query: 423 QGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           QGY VA+TLETTEAE+M T+F HPTLSE MHESVL AYGRA+HF
Sbjct: 419 QGYVVAKTLETTEAELMHTVFAHPTLSEMMHESVLDAYGRAVHF 462


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: 696
Number of extensions: 32
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: 466
Length of database: 462
Length adjustment: 33
Effective length of query: 433
Effective length of database: 429
Effective search space:   185757
Effective search space used:   185757
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 WP_011384718.1 AMB_RS11730 (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.19156.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-173  561.6   8.4   7.2e-173  561.4   8.4    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011384718.1  AMB_RS11730 dihydrolipoyl dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011384718.1  AMB_RS11730 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.4   8.4  7.2e-173  7.2e-173       2     461 .]       6     462 .]       5     462 .] 0.98

  Alignments for each domain:
  == domain 1  score: 561.4 bits;  conditional E-value: 7.2e-173
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                               +d++viGgGpgGYvaAiraaqlg+++alve+e+lGG+Cln+GCiPtKalL+sae+++++++a+++g+++
  lcl|NCBI__GCF_000009985.1:WP_011384718.1   6 FDIIVIGGGPGGYVAAIRAAQLGMNTALVEREHLGGICLNWGCIPTKALLRSAEIYRNMQHAESYGLSA 74 
                                               9******************************************************************** PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAt 139
                                                + ++dl+k+++r++ v+ +l+gGvk+Llkknkv+vi+G+akl + ++v ++++    +++a +ii+At
  lcl|NCBI__GCF_000009985.1:WP_011384718.1  75 PGATFDLAKIVARSRGVSAQLQGGVKHLLKKNKVTVIEGTAKLAGGSKVAIEGKP---TISAPHIILAT 140
                                               *****************************************************97...79********* PP

                                 TIGR01350 140 GseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpa 208
                                               G++ r lp+ +e d+k+++t++eal  +++p++l+++G+G+iG+Efas+f+ lG++vtv e++dr+lp+
  lcl|NCBI__GCF_000009985.1:WP_011384718.1 141 GARARILPG-FEPDGKFIWTYKEALVPDTMPKRLLVIGSGAIGIEFASFFNALGAQVTVAEAMDRVLPV 208
                                               *********.*********************************************************** PP

                                 TIGR01350 209 ldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgl 276
                                               +dae+s +++k+++k+g+kil +a+++ ++k++ +v+v+++ + +++++++++++ a+G   n+e++gl
  lcl|NCBI__GCF_000009985.1:WP_011384718.1 209 EDAEISAMAQKSFEKQGMKILAGANIKGLKKNAVDVTVTIEAGgKTHEVTVDRIITAIGIVGNVENVGL 277
                                               *************************************888877799*********************** PP

                                 TIGR01350 277 eklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPs 344
                                               e++  ++++   + +de++rt  pg+yaiGD++g + LAh+As+e+++++eki g  +   +d++++P 
  lcl|NCBI__GCF_000009985.1:WP_011384718.1 278 EATKAKVER-THVITDEYCRTGEPGLYAIGDIAGAPWLAHKASHEAIICVEKIKGLPDVhPLDMRKIPG 345
                                               ******988.7799*****************************************988779******** PP

                                 TIGR01350 345 viytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaea 413
                                               ++y++P+vasvGl+e++ake+g++vkvg+fpf+angka+al+et+G++k+++d ktge+lGah++gae+
  lcl|NCBI__GCF_000009985.1:WP_011384718.1 346 CTYCHPQVASVGLSEAKAKEKGYAVKVGRFPFMANGKAIALGETEGMIKTVFDAKTGELLGAHMIGAEV 414
                                               ********************************************************************* PP

                                 TIGR01350 414 seliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               +eli+  ++a +le+t+ el++t+++HPtlsE+++e++l+a+g+a+h+
  lcl|NCBI__GCF_000009985.1:WP_011384718.1 415 TELIQGYVVAKTLETTEAELMHTVFAHPTLSEMMHESVLDAYGRAVHF 462
                                               *********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (462 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: 00:00:00.01
# Mc/sec: 11.08
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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