Alignments for a candidate for lpd in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Halomonas desiderata SP1

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_086510769.1 BZY95_RS15335 dihydrolipoyl dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_002151265.1:WP_086510769.1
          Length = 478

 Score =  639 bits (1648), Expect = 0.0
 Identities = 316/478 (66%), Positives = 388/478 (81%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           M+ KFDV+VIGAGPGGYVAAIRAAQLGLKTAC+EK++ KEGK   GGTCLNVGCIPSKAL
Sbjct: 1   MADKFDVIVIGAGPGGYVAAIRAAQLGLKTACVEKWVNKEGKTVHGGTCLNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           L++S+K+ EA++ F   GI+ +    +V  M+  K +++    GGI+ LFKANGVT+ +G
Sbjct: 61  LETSHKFVEARDHFAEIGIDLEPPKANVAKMLEFKNSVIAKNVGGISALFKANGVTAIDG 120

Query: 121 HGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALEFQAV 180
            GK++A KQVEVT  DG     EA+N++IA+GS PVEIPP PL +DI+V STGALEF  V
Sbjct: 121 TGKVVAAKQVEVTDHDGGKTTYEADNIVIAAGSVPVEIPPTPLHEDIVVTSTGALEFTEV 180

Query: 181 PKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQGLNIR 240
           PK+LGVIGAGVIGLELGSVW+RLGAEVTVLEA+D FLP  D  IAKE  K+L KQGL+I+
Sbjct: 181 PKRLGVIGAGVIGLELGSVWSRLGAEVTVLEAMDTFLPMVDTAIAKETQKLLKKQGLDIK 240

Query: 241 LGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGVTLDERGF 300
           LGARVT SEVK  +VTV ++D NGEQ++TFDKLIV VGRRP T  ++  + GV LDERGF
Sbjct: 241 LGARVTGSEVKGNEVTVKYSDGNGEQEQTFDKLIVCVGRRPYTKGVVDENVGVGLDERGF 300

Query: 301 IYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPSVIYTH 360
           I+VDD C+TSVPG++AIGD VRG MLAHKASEEGVMVA+ IAGHKA+MNYD IPSVIYT 
Sbjct: 301 IHVDDQCRTSVPGIYAIGDCVRGPMLAHKASEEGVMVADIIAGHKAEMNYDAIPSVIYTS 360

Query: 361 PEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVLGVHVI 420
           PE+AWVG  EQ  KA+G++V  G+FPF+A+GRA+A N   G+ KVIADA+TDR+LG+H++
Sbjct: 361 PEVAWVGMNEQEAKAKGIKVKTGSFPFSANGRALANNAPEGMAKVIADAETDRILGMHIV 420

Query: 421 GPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIHIANRKKR 478
              A EL+ QG I MEFG+SAEDL +  ++HP+ SEA+HEAALAV+GHAIH+ANRKKR
Sbjct: 421 SQHAGELIAQGVIAMEFGSSAEDLALTCYAHPSTSEAIHEAALAVDGHAIHMANRKKR 478


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: 790
Number of extensions: 35
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: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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_086510769.1 BZY95_RS15335 (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.26776.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-168  545.1  12.0   7.2e-168  544.9  12.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510769.1  BZY95_RS15335 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510769.1  BZY95_RS15335 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.9  12.0  7.2e-168  7.2e-168       1     461 []       4     472 ..       4     472 .. 0.96

  Alignments for each domain:
  == domain 1  score: 544.9 bits;  conditional E-value: 7.2e-168
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek..ek.....lGGtClnvGCiPtKalLksaevveelke 62 
                                               ++dv+viG+GpgGYvaAiraaqlglk+a+vek  +k      GGtClnvGCiP+KalL++++ + e+++
  lcl|NCBI__GCF_002151265.1:WP_086510769.1   4 KFDVIVIGAGPGGYVAAIRAAQLGLKTACVEKwvNKegktvHGGTCLNVGCIPSKALLETSHKFVEARD 72 
                                               59****************************9765332333379*********************99999 PP

                                 TIGR01350  63 .akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kk 129
                                                ++e+gi++e  k +++k+le k++v+ k vgG++aL+k n+v+ i G++k++ +k+vev+++++  ++
  lcl|NCBI__GCF_002151265.1:WP_086510769.1  73 hFAEIGIDLEPPKANVAKMLEFKNSVIAKNVGGISALFKANGVTAIDGTGKVVAAKQVEVTDHDGGkTT 141
                                               8************************************************************99876589 PP

                                 TIGR01350 130 leakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtv 198
                                               +ea+ni+iA Gs p e+p     +e++v+ts++ale++evp++l ++G+GviG+E++s++++lG++vtv
  lcl|NCBI__GCF_002151265.1:WP_086510769.1 142 YEADNIVIAAGSVPVEIPP-TPLHEDIVVTSTGALEFTEVPKRLGVIGAGVIGLELGSVWSRLGAEVTV 209
                                               9*****************9.7777778****************************************** PP

                                 TIGR01350 199 ielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavG 266
                                               +e++d+ lp++d+ ++k+ +k lkk+g++i+ +a+vt  e + +ev+v+ +++  +++ + +k++v+vG
  lcl|NCBI__GCF_002151265.1:WP_086510769.1 210 LEAMDTFLPMVDTAIAKETQKLLKKQGLDIKLGARVTGSEVKGNEVTVKYSDGnGEQEQTFDKLIVCVG 278
                                               *************************************88888888887766665679999********* PP

                                 TIGR01350 267 rkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks 335
                                               r+p ++++  e++gv lderg+i+vd+++rt+vpgiyaiGD+++++mLAh+As+egv++a+ iag+++ 
  lcl|NCBI__GCF_002151265.1:WP_086510769.1 279 RRPYTKGVVDENVGVGLDERGFIHVDDQCRTSVPGIYAIGDCVRGPMLAHKASEEGVMVADIIAGHKA- 346
                                               *****************************************************************665. PP

                                 TIGR01350 336 eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeil 404
                                               e++y+a+Psviyt+Peva vG++e++ak++gi+vk+g+fpf+ang+ala +  +G++kvi+d +t++il
  lcl|NCBI__GCF_002151265.1:WP_086510769.1 347 EMNYDAIPSVIYTSPEVAWVGMNEQEAKAKGIKVKTGSFPFSANGRALANNAPEGMAKVIADAETDRIL 415
                                               9******************************************************************** PP

                                 TIGR01350 405 GahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               G+hiv+++a eli++ ++a+e++ ++e+la t+++HP+ sEai+eaala+ g+aih+
  lcl|NCBI__GCF_002151265.1:WP_086510769.1 416 GMHIVSQHAGELIAQGVIAMEFGSSAEDLALTCYAHPSTSEAIHEAALAVDGHAIHM 472
                                               ********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (478 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: 00:00:00.02
# Mc/sec: 10.66
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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