Alignments for a candidate for lpd in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Marinobacter adhaerens HP15

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate GFF1561 HP15_1523 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__Marino:GFF1561
          Length = 480

 Score =  679 bits (1753), Expect = 0.0
 Identities = 334/479 (69%), Positives = 403/479 (84%), Gaps = 1/479 (0%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKV-ALGGTCLNVGCIPSKA 59
           MS K+DV+VIGAGPGGYVAAI+AAQLGLKTAC+E +  ++GK   LGGTCLNVGCIPSKA
Sbjct: 1   MSDKYDVIVIGAGPGGYVAAIKAAQLGLKTACVESWTSEDGKAQVLGGTCLNVGCIPSKA 60

Query: 60  LLDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFE 119
           LL+ S+K+ E+   F++ GI AK V +D+  M+ RK+ IVK LTGGIA LFK+NGVTS  
Sbjct: 61  LLEISHKFEESSHDFEMQGIIAKDVKMDIGKMMERKSGIVKQLTGGIAGLFKSNGVTSIH 120

Query: 120 GHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQA 179
           GHGKLLAN++VEVT  DGK++  EAEN+I+A+GS+P++IPPAP   + IVDS GALEF  
Sbjct: 121 GHGKLLANRKVEVTDKDGKSKTYEAENIILATGSKPIQIPPAPFDGEYIVDSEGALEFTE 180

Query: 180 VPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNI 239
           VPK+LGVIGAGVIGLELGSVWARLGAEVTVLEA D FLPA D+Q+AK+ALK   KQGLNI
Sbjct: 181 VPKRLGVIGAGVIGLELGSVWARLGAEVTVLEAQDTFLPAVDQQVAKDALKQFQKQGLNI 240

Query: 240 RLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERG 299
            +GAR+T +EVK+K V V + D+ G+ +  FDKLIVAVGRRP T +LL+ DSGV +DERG
Sbjct: 241 VMGARMTGAEVKRKLVNVNYEDSKGKHEAKFDKLIVAVGRRPYTDNLLSEDSGVQMDERG 300

Query: 300 FIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYT 359
           FI+VDD+CKT  PGV+AIGDVVRG MLAHKASEEG+MVAERIAGHK Q+NYD IP+V+YT
Sbjct: 301 FIFVDDNCKTEAPGVWAIGDVVRGPMLAHKASEEGIMVAERIAGHKPQVNYDCIPNVVYT 360

Query: 360 HPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHV 419
            PE+AWVGKTE+ +KAEG E NVGTFPFAA+GRAMAAN  +GLVK+IADAKTDR++G HV
Sbjct: 361 FPEVAWVGKTEEQMKAEGEEYNVGTFPFAANGRAMAANSASGLVKIIADAKTDRIVGFHV 420

Query: 420 IGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIANRKKR 478
           +GP A+E+V QG I MEFG+SAEDL +  F+HPTLSE++HEAALAV G AIHIANR+K+
Sbjct: 421 VGPQASEIVAQGVIAMEFGSSAEDLALTCFAHPTLSESVHEAALAVGGGAIHIANRRKK 479


Lambda     K      H
   0.316    0.134    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: 791
Number of extensions: 29
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: 478
Length of database: 480
Length adjustment: 34
Effective length of query: 444
Effective length of database: 446
Effective search space:   198024
Effective search space used:   198024
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 GFF1561 HP15_1523 (dihydrolipoamide 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.12435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.2e-169  548.4   6.5   7.1e-169  548.2   6.5    1.0  1  lcl|FitnessBrowser__Marino:GFF1561  HP15_1523 dihydrolipoamide dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1561  HP15_1523 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.2   6.5  7.1e-169  7.1e-169       1     461 []       4     473 ..       4     473 .. 0.96

  Alignments for each domain:
  == domain 1  score: 548.2 bits;  conditional E-value: 7.1e-169
                           TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalve.......k.eklGGtClnvGCiPtKalLksaevveelke.akel 66 
                                         +ydv+viG+GpgGYvaAi+aaqlglk+a+ve       k + lGGtClnvGCiP+KalL+ ++ +ee ++ ++  
  lcl|FitnessBrowser__Marino:GFF1561   4 KYDVIVIGAGPGGYVAAIKAAQLGLKTACVEswtsedgKaQVLGGTCLNVGCIPSKALLEISHKFEESSHdFEMQ 78 
                                         59****************************9555544433569***************************9**** PP

                           TIGR01350  67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtG 140
                                         gi +++vk+d+ k++erk+ +vk+l+gG+++L+k+n+v++i+G++kll +++vev++++++ k++ea+nii+AtG
  lcl|FitnessBrowser__Marino:GFF1561  79 GIIAKDVKMDIGKMMERKSGIVKQLTGGIAGLFKSNGVTSIHGHGKLLANRKVEVTDKDGKsKTYEAENIILATG 153
                                         **9999***************************************************998889************ PP

                           TIGR01350 141 seprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevsk 215
                                         s+p+++p    +d++++++se+ale++evp++l ++G+GviG+E++s++a+lG++vtv+e++d+ lpa+d++v+k
  lcl|FitnessBrowser__Marino:GFF1561 154 SKPIQIPP-APFDGEYIVDSEGALEFTEVPKRLGVIGAGVIGLELGSVWARLGAEVTVLEAQDTFLPAVDQQVAK 227
                                         *******9.8999999*********************************************************** PP

                           TIGR01350 216 vlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergai 289
                                          + k+++k+g++i+++a++t  e +++ v v+ +++  +++ + +k++vavGr+p +++l  e  gv++derg+i
  lcl|FitnessBrowser__Marino:GFF1561 228 DALKQFQKQGLNIVMGARMTGAEVKRKLVNVNYEDSkGKHEAKFDKLIVAVGRRPYTDNLLSEDSGVQMDERGFI 302
                                         ********************8888888888766666567999********************************* PP

                           TIGR01350 290 kvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqake 364
                                          vd++++t++pg++aiGDv++++mLAh+As+eg+++ae+iag+++ +++y+ +P+v+yt Peva vG+teeq+k+
  lcl|FitnessBrowser__Marino:GFF1561 303 FVDDNCKTEAPGVWAIGDVVRGPMLAHKASEEGIMVAERIAGHKP-QVNYDCIPNVVYTFPEVAWVGKTEEQMKA 376
                                         ******************************************888.9**************************** PP

                           TIGR01350 365 egievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihp 439
                                         eg e++vg fpfaang+a+a++ ++G+vk+i+d kt++i+G+h+vg++ase++++ ++a+e++ ++e+la t+++
  lcl|FitnessBrowser__Marino:GFF1561 377 EGEEYNVGTFPFAANGRAMAANSASGLVKIIADAKTDRIVGFHVVGPQASEIVAQGVIAMEFGSSAEDLALTCFA 451
                                         *************************************************************************** PP

                           TIGR01350 440 HPtlsEaikeaalaalgkaihv 461
                                         HPtlsE ++eaala+ g aih+
  lcl|FitnessBrowser__Marino:GFF1561 452 HPTLSESVHEAALAVGGGAIHI 473
                                         *****************99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (480 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: 00:00:00.02
# Mc/sec: 9.61
//
[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