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 (EC 1.8.1.4) (characterized)
to candidate GFF65 HP15_65 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0H2ZB32
         (464 letters)



>FitnessBrowser__Marino:GFF65
          Length = 461

 Score =  514 bits (1324), Expect = e-150
 Identities = 268/466 (57%), Positives = 337/466 (72%), Gaps = 9/466 (1%)

Query: 1   MSQILKTSLLIVGGGPGGYVAAIRAGQLGIPTVLVEGAALGGTCLNVGCIPSKALIHAAE 60
           MS+++KT +L+VGGGPGGYVAAIR GQLG+ TVLVE   LGGTCL  GCIPSKA+IHAA 
Sbjct: 1   MSEVIKTKVLVVGGGPGGYVAAIRCGQLGLDTVLVEADQLGGTCLTRGCIPSKAMIHAAS 60

Query: 61  EYLKARHYAGRSALGIQV-QAPSIDIARTVEWKDAIVDRLTSGVAALLKKHGVDVVQGWA 119
           E+      A +  LGI + + P +D+A TV+WKD+IV RL +GVAALLK+  V VV+GW 
Sbjct: 61  EFSAMMKAASKPHLGISLSEPPKVDLAATVDWKDSIVKRLNTGVAALLKRAKVKVVKGWG 120

Query: 120 RILDGKSVAVELAGGGSQRIECEHLLLAAGSQSVELPILPLGGKVISSTEALAPGSLPKR 179
              D K+  VE A G    I+ EH++LA GS  VELP LPLGGKVISSTEAL+   +P +
Sbjct: 121 TFSDAKTCNVETADGVIT-IQSEHVILATGSAPVELPFLPLGGKVISSTEALSLPDVPSK 179

Query: 180 LVVVGGGYIGLELGTAYRKLGVEVAVVEAQPRILPGYDEELTKPVAQALRKLGVELYLGH 239
           LVV+G GYIGLELG AY KLG +V +VE+  RILP YDE L +PV + L +  V+L+L  
Sbjct: 180 LVVIGAGYIGLELGIAYAKLGSDVTIVESSDRILPLYDEALVEPVRRWLDESAVKLHLNA 239

Query: 240 SLLGPSENGVRVRDGAGEEREIAADQVLVAVGRKPRSEGWNLESLGLDMNGRAVKVDDQC 299
             LG  + G+ V    G E  + AD +LV VGRKP ++GW LE++ LDM+GR V+VD+QC
Sbjct: 240 RALGERDGGLAVELEGGSETVLPADNILVTVGRKPVTQGWGLENMALDMDGRYVRVDEQC 299

Query: 300 RTSMRNVWAIGDLAGEPMLAHRAMAQGEMVAELIAGKRRQFAPVAIPAVCFTDPEVVVAG 359
            TSM+NVWAIGDL GEPMLAH+A AQGE+VAE+IAGKRR+F PVAIPAVCFT+PE+V  G
Sbjct: 300 ATSMKNVWAIGDLVGEPMLAHKASAQGEVVAEVIAGKRRRFDPVAIPAVCFTEPEIVSVG 359

Query: 360 LSPEQAKDAGLDCLVASFPFAANGRAMTLEA--NEGFVRVVARRDNHLVVGWQAVGKAVS 417
             P  A       +   FP AANGRA++++A  N GFVRVVA  + H ++G QAVG  +S
Sbjct: 360 AEPSLA-----GTVTGVFPVAANGRALSMDAGDNGGFVRVVAHSETHRILGVQAVGTHIS 414

Query: 418 ELSTAFAQSLEMGARLEDIAGTIHAHPTLGEAVQEAALRALGHALH 463
           EL+ AF  ++EMGA ++DI G I AHPTLGE   EA+L+ LGHA+H
Sbjct: 415 ELTAAFVTAVEMGATVDDIEGMIQAHPTLGEMFHEASLKILGHAIH 460


Lambda     K      H
   0.318    0.136    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: 670
Number of extensions: 36
Number of successful extensions: 8
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: 464
Length of database: 461
Length adjustment: 33
Effective length of query: 431
Effective length of database: 428
Effective search space:   184468
Effective search space used:   184468
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF65 HP15_65 (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.7323.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.3e-142  459.4   1.2   7.1e-142  459.2   1.2    1.0  1  lcl|FitnessBrowser__Marino:GFF65  HP15_65 dihydrolipoamide dehydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF65  HP15_65 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.2   1.2  7.1e-142  7.1e-142       3     460 ..       8     460 ..       6     461 .] 0.95

  Alignments for each domain:
  == domain 1  score: 459.2 bits;  conditional E-value: 7.1e-142
                         TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke.ak..elgieven.vkl 75 
                                        v+v+GgGpgGYvaAir++qlgl ++lve ++lGGtCl +GCiP+Ka++++a  ++ + + a+  +lgi++++  k+
  lcl|FitnessBrowser__Marino:GFF65   8 KVLVVGGGPGGYVAAIRCGQLGLDTVLVEADQLGGTCLTRGCIPSKAMIHAASEFSAMMKaASkpHLGISLSEpPKV 84 
                                       799************************************************9988877664432269***9998*** PP

                         TIGR01350  76 dlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplklee 152
                                       dl++ +++k+++vk+l++Gv+aLlk++kv+v+kG ++++d+k+ +v++ ++  +++ +++i+AtGs p elp+ l  
  lcl|FitnessBrowser__Marino:GFF65  85 DLAATVDWKDSIVKRLNTGVAALLKRAKVKVVKGWGTFSDAKTCNVETADGVITIQSEHVILATGSAPVELPF-LPL 160
                                       **************************************************99*********************.999 PP

                         TIGR01350 153 dekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkil 229
                                        +  vi+s+eal+l+ vp++lv++G+G+iG+E++ ++aklG++vt++e +drilp  d+ + + +++ l ++ vk++
  lcl|FitnessBrowser__Marino:GFF65 161 GG-KVISSTEALSLPDVPSKLVVIGAGYIGLELGIAYAKLGSDVTIVESSDRILPLYDEALVEPVRRWLDESAVKLH 236
                                       88.59************************************************************************ PP

                         TIGR01350 230 tnakvtevekeedevvveakkkevetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiG 306
                                        na+     +++  + ve +++ +++l a+++Lv+vGrkp +++ gle++ +++d   ++ vde++ t++++++aiG
  lcl|FitnessBrowser__Marino:GFF65 237 LNARAL--GERDGGLAVELEGGSETVLPADNILVTVGRKPVTQGWGLENMALDMDG-RYVRVDEQCATSMKNVWAIG 310
                                       ***988..78888888888899889*******************************.67****************** PP

                         TIGR01350 307 DvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkal 383
                                       D++g++mLAh+As++g v+ae iagk++  +d  a+P+v +tePe+ svG   + a       ++g fp+aang+al
  lcl|FitnessBrowser__Marino:GFF65 311 DLVGEPMLAHKASAQGEVVAEVIAGKRR-RFDPVAIPAVCFTEPEIVSVGAEPSLA-----GTVTGVFPVAANGRAL 381
                                       *************************887.9********************877655.....45799*********** PP

                         TIGR01350 384 alee..tdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgka 458
                                       +++   + Gfv+v+++ +t++ilG++ vg++ sel + ++ ave+++tv++++ +i++HPtl+E+++ea l++lg+a
  lcl|FitnessBrowser__Marino:GFF65 382 SMDAgdNGGFVRVVAHSETHRILGVQAVGTHISELTAAFVTAVEMGATVDDIEGMIQAHPTLGEMFHEASLKILGHA 458
                                       99754388********************************************************************* PP

                         TIGR01350 459 ih 460
                                       ih
  lcl|FitnessBrowser__Marino:GFF65 459 IH 460
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (461 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.46
//
[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