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, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate WP_011386317.1 AMB_RS20050 dihydrolipoyl dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>NCBI__GCF_000009985.1:WP_011386317.1
          Length = 469

 Score =  580 bits (1496), Expect = e-170
 Identities = 285/462 (61%), Positives = 352/462 (76%)

Query: 39  DVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 98
           DVVIIGGGPGGYVAAI+AAQLG KT CIEKRG+LGGTCLNVGCIPSKALL +SH YH A 
Sbjct: 7   DVVIIGGGPGGYVAAIRAAQLGLKTACIEKRGSLGGTCLNVGCIPSKALLTASHHYHAAA 66

Query: 99  HSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPSEIS 158
           H   + G+KV+ VE+D+A MMG KDK VS+ T+GIE LFKKNKVTY+ G G   +P +I 
Sbjct: 67  HELGSFGIKVAKVEMDVAGMMGHKDKVVSDNTKGIEFLFKKNKVTYIVGAGAITAPGQIE 126

Query: 159 VDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIGAGY 218
           V   +G  + V  KHI+IATGSDV  LPGV IDE+ I+SSTGALALS+ PK +VVIG G 
Sbjct: 127 VTAKDGAKSNVAAKHIVIATGSDVTPLPGVEIDEEVIISSTGALALSKTPKHMVVIGGGV 186

Query: 219 IGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGVDTS 278
           IGLE+G+VWGR+G++VTVVEF   I+P  D E+ KQ QR L KQGM+FKL TKV G+   
Sbjct: 187 IGLELGTVWGRLGAKVTVVEFLDRILPFNDGEVSKQMQRLLAKQGMEFKLGTKVTGIAKK 246

Query: 279 GDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNERFST 338
           G    +TVEP+AGG    IEAD VLV+ GR P+T GL LDK+GV  DK G + ++  F T
Sbjct: 247 GKTATVTVEPAAGGAAEKIEADSVLVAIGRKPYTEGLGLDKVGVALDKRGFVQIDGHFRT 306

Query: 339 NVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASVGKT 398
           NV G+YAIGDV+ G MLAHKAEE+GVA  E LAG+ GHV+Y+ +P VVYT PEVASVGKT
Sbjct: 307 NVPGIYAIGDVVGGAMLAHKAEEEGVALAEILAGQHGHVNYEAIPAVVYTWPEVASVGKT 366

Query: 399 EEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGELIH 458
           EEQ+K  G+ Y+ GKFPF AN RA++++  +G VK++A   TDK+LG HI+ PNAG+LI 
Sbjct: 367 EEQLKAEGIAYKAGKFPFTANGRARSMNEVDGFVKVLACATTDKVLGAHIVGPNAGDLIA 426

Query: 459 EAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIH 500
           E  +A+++ A+SEDIAR CHAHP + EA+KEA +A   +P+H
Sbjct: 427 EVVLAMEFGAASEDIARTCHAHPGLGEAVKEACLAVDGRPLH 468


Lambda     K      H
   0.315    0.133    0.370 

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: 719
Number of extensions: 27
Number of successful extensions: 1
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: 501
Length of database: 469
Length adjustment: 34
Effective length of query: 467
Effective length of database: 435
Effective search space:   203145
Effective search space used:   203145
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_011386317.1 AMB_RS20050 (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.19330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-181  589.6  14.4   2.3e-181  589.4  14.4    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386317.1  AMB_RS20050 dihydrolipoyl dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386317.1  AMB_RS20050 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.4  14.4  2.3e-181  2.3e-181       2     460 ..       6     468 ..       5     469 .] 0.97

  Alignments for each domain:
  == domain 1  score: 589.4 bits;  conditional E-value: 2.3e-181
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgi 68 
                                               +dvv+iGgGpgGYvaAiraaqlglk+a++ek  +lGGtClnvGCiP+KalL++++ ++ + + + ++gi
  lcl|NCBI__GCF_000009985.1:WP_011386317.1   6 FDVVIIGGGPGGYVAAIRAAQLGLKTACIEKrGSLGGTCLNVGCIPSKALLTASHHYHAAAHeLGSFGI 74 
                                               9******************************889****************************9****** PP

                                 TIGR01350  69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleaknii 136
                                               +v++v++d++ ++ +k+kvv+  ++G+++L+kknkv+ i G + ++ ++++ev++++++ +++ ak+i+
  lcl|NCBI__GCF_000009985.1:WP_011386317.1  75 KVAKVEMDVAGMMGHKDKVVSDNTKGIEFLFKKNKVTYIVGAGAITAPGQIEVTAKDGAkSNVAAKHIV 143
                                               *******************************************************998868899***** PP

                                 TIGR01350 137 iAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldri 205
                                               iAtGs+++ lp+ +e de+v+i+s++al+l+++p+++v++GgGviG+E+++++ +lG+kvtv+e+ldri
  lcl|NCBI__GCF_000009985.1:WP_011386317.1 144 IATGSDVTPLPG-VEIDEEVIISSTGALALSKTPKHMVVIGGGVIGLELGTVWGRLGAKVTVVEFLDRI 211
                                               ************.******************************************************** PP

                                 TIGR01350 206 lpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnl 271
                                               lp++d evsk++++ l k+g++++ ++kvt + k+ ++ +  ve   +  +e++ea+ vLva+Grkp +
  lcl|NCBI__GCF_000009985.1:WP_011386317.1 212 LPFNDGEVSKQMQRLLAKQGMEFKLGTKVTGIAKKGKTATvtVEPAAGgAAEKIEADSVLVAIGRKPYT 280
                                               ******************************877776665533666555689****************** PP

                                 TIGR01350 272 eelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidyk 340
                                               e+lgl+k+gv ld+rg++++d ++rtnvpgiyaiGDv+g++mLAh+A++egv  ae +ag++  +++y+
  lcl|NCBI__GCF_000009985.1:WP_011386317.1 281 EGLGLDKVGVALDKRGFVQIDGHFRTNVPGIYAIGDVVGGAMLAHKAEEEGVALAEILAGQHG-HVNYE 348
                                               ************************************************************998.9**** PP

                                 TIGR01350 341 avPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahiv 409
                                               a+P+v+yt PevasvG+teeq+k+egi++k+gkfpf+ang+a++++e dGfvkv++  +t+++lGahiv
  lcl|NCBI__GCF_000009985.1:WP_011386317.1 349 AIPAVVYTWPEVASVGKTEEQLKAEGIAYKAGKFPFTANGRARSMNEVDGFVKVLACATTDKVLGAHIV 417
                                               ********************************************************************* PP

                                 TIGR01350 410 gaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               g++a +li+e++la+e+++ +e++a+t+h+HP l+Ea+kea+la+ g+++h
  lcl|NCBI__GCF_000009985.1:WP_011386317.1 418 GPNAGDLIAEVVLAMEFGAASEDIARTCHAHPGLGEAVKEACLAVDGRPLH 468
                                               ************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (469 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.92
//
[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