Alignments for a candidate for lpd in Oleispira antarctica

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Oleispira antarctica

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate WP_046008884.1 OLEAN_RS08545 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_015561
         (478 letters)



>NCBI__GCF_000967895.1:WP_046008884.1
          Length = 481

 Score =  695 bits (1793), Expect = 0.0
 Identities = 348/478 (72%), Positives = 406/478 (84%)

Query: 1   MTQKFDVVVIGAGPGGYVAAIKAAQLGLKTACIEKYTDAEGKLALGGTCLNVGCIPSKAL 60
           M+++FDVVVIG GPGGYVAAI+ AQLGL TACI+K+ + EGK   GGTCLNVGCIPSKAL
Sbjct: 1   MSKQFDVVVIGGGPGGYVAAIRCAQLGLSTACIDKWVNKEGKGVFGGTCLNVGCIPSKAL 60

Query: 61  LDSSWKYKEAKESFNVHGISTGEVKMDVAAMVGRKAGIVKNLTGGVATLFKANGVTSIQG 120
           LDS+ KY+EA E F +HGI+ GEVKMDV AMV RK  IVKNLT GVATLFKANGVT+++G
Sbjct: 61  LDSTHKYEEAHEKFALHGITMGEVKMDVPAMVQRKDQIVKNLTMGVATLFKANGVTALEG 120

Query: 121 HGKLLAGKKVEVTKADGTTEVIEAENVILASGSRPIDIPPAPVDQNVIVDSTGALEFQAV 180
            GKLLAG+KVE T   G +E+IEAENVILA+GS P++IPP P+  N+IVDSTGALEF  V
Sbjct: 121 TGKLLAGRKVEFTNHAGVSEIIEAENVILATGSVPVEIPPTPLTDNIIVDSTGALEFTEV 180

Query: 181 PKRLGVIGAGVIGLELGSVWARLGAEVTVLEALDTFLMAADTAVSKEAQKTLTKQGLDIK 240
           PKRLGVIGAGVIGLELGSVW RLG+EV VLEA D+FL   D AV+KEA+K LTKQGLDI+
Sbjct: 181 PKRLGVIGAGVIGLELGSVWNRLGSEVVVLEAQDSFLHTVDQAVAKEAKKLLTKQGLDIR 240

Query: 241 LGARVTGSKVNGNEVEVTYTNAEGEQKITFDKLIVAVGRRPVTTDLLAADSGVTIDERGY 300
           +GARVTGS+VNG+EV VTY ++EGEQKITFDKLIVAVGRRP T  LLA DSGV +DERG+
Sbjct: 241 IGARVTGSEVNGDEVTVTYQDSEGEQKITFDKLIVAVGRRPYTEGLLAGDSGVNMDERGF 300

Query: 301 IFVDDYCATSVPGVYAIGDVVRGMMLAHKASEEGIMVVERIKGHKAQMNYDLIPSVIYTH 360
           +FV+ YC+T  PG++AIGDVVRG MLAHKASEEG+MV ERI GHKAQ+NYD++PSVIYT 
Sbjct: 301 LFVNHYCSTDAPGIWAIGDVVRGPMLAHKASEEGVMVAERIAGHKAQLNYDVVPSVIYTS 360

Query: 361 PEIAWVGKTEQALKAEGVEVNVGTFPFAASGRAMAANDTGGFVKVIADAKTDRVLGVHVI 420
           PEIA VG TE+ LKA G   NVG FPFAA+GRAMA+ DT GFVK+IADA+TDR+LG H+I
Sbjct: 361 PEIASVGHTEEQLKANGESYNVGMFPFAANGRAMASTDTEGFVKIIADAETDRILGAHII 420

Query: 421 GPSAAELVQQGAIAMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGGAIHVANRKKR 478
           GP+A +L QQ  IAMEFG+SAED+GMMVF+HPT+SE +HEAALAVN  AIH ANRK +
Sbjct: 421 GPNAGDLCQQIVIAMEFGSSAEDIGMMVFAHPTISETVHEAALAVNNSAIHKANRKPK 478


Lambda     K      H
   0.316    0.133    0.374 

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: 795
Number of extensions: 26
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: 478
Length of database: 481
Length adjustment: 34
Effective length of query: 444
Effective length of database: 447
Effective search space:   198468
Effective search space used:   198468
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: 51 (24.3 bits)

Align candidate WP_046008884.1 OLEAN_RS08545 (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.3846.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-165  536.5   8.3   2.9e-165  536.3   8.3    1.0  1  lcl|NCBI__GCF_000967895.1:WP_046008884.1  OLEAN_RS08545 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000967895.1:WP_046008884.1  OLEAN_RS08545 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.3   8.3  2.9e-165  2.9e-165       1     460 [.       4     471 ..       4     472 .. 0.96

  Alignments for each domain:
  == domain 1  score: 536.3 bits;  conditional E-value: 2.9e-165
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevveelke 62 
                                               ++dvvviGgGpgGYvaAir+aqlgl++a+++k  +k     +GGtClnvGCiP+KalL s++ +ee++e
  lcl|NCBI__GCF_000967895.1:WP_046008884.1   4 QFDVVVIGGGPGGYVAAIRCAQLGLSTACIDKwvNKegkgvFGGTCLNVGCIPSKALLDSTHKYEEAHE 72 
                                               59***************************99765323444489*************************9 PP

                                 TIGR01350  63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kk 129
                                                ++ +gi++ +vk+d+ ++++rk+++vk+l+ Gv++L+k n+v+ ++G++kll  ++ve +++++  + 
  lcl|NCBI__GCF_000967895.1:WP_046008884.1  73 kFALHGITMGEVKMDVPAMVQRKDQIVKNLTMGVATLFKANGVTALEGTGKLLAGRKVEFTNHAGVsEI 141
                                               9************************************************************99987799 PP

                                 TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198
                                               +ea+n+i+AtGs p e+p       +++++s++ale++evp++l ++G+GviG+E++s++++lG++v v
  lcl|NCBI__GCF_000967895.1:WP_046008884.1 142 IEAENVILATGSVPVEIPP-TPLTDNIIVDSTGALEFTEVPKRLGVIGAGVIGLELGSVWNRLGSEVVV 209
                                               9*****************9.7777789****************************************** PP

                                 TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavG 266
                                               +e++d  l ++d+ v+k++kk l+k+g++i  +a+vt  e + dev+v+ +++  +++++ +k++vavG
  lcl|NCBI__GCF_000967895.1:WP_046008884.1 210 LEAQDSFLHTVDQAVAKEAKKLLTKQGLDIRIGARVTGSEVNGDEVTVTYQDSeGEQKITFDKLIVAVG 278
                                               *************************************99999999996666665679************ PP

                                 TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks 335
                                               r+p +e+l     gv++derg++ v++++ t +pgi+aiGDv++++mLAh+As+egv++ae+iag+++ 
  lcl|NCBI__GCF_000967895.1:WP_046008884.1 279 RRPYTEGLLAGDSGVNMDERGFLFVNHYCSTDAPGIWAIGDVVRGPMLAHKASEEGVMVAERIAGHKA- 346
                                               *****************************************************************665. PP

                                 TIGR01350 336 eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeil 404
                                               +++y++vPsviyt+Pe+asvG teeq+k++g +++vg fpfaang+a+a+ +t+Gfvk+i+d +t++il
  lcl|NCBI__GCF_000967895.1:WP_046008884.1 347 QLNYDVVPSVIYTSPEIASVGHTEEQLKANGESYNVGMFPFAANGRAMASTDTEGFVKIIADAETDRIL 415
                                               9******************************************************************** PP

                                 TIGR01350 405 GahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                               Gahi+g++a +l +++++a+e++ ++e++ +++++HPt+sE+++eaala++++aih
  lcl|NCBI__GCF_000967895.1:WP_046008884.1 416 GAHIIGPNAGDLCQQIVIAMEFGSSAEDIGMMVFAHPTISETVHEAALAVNNSAIH 471
                                               ******************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (481 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: 12.02
//
[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