Alignments for a candidate for lpd in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Stenotrophomonas chelatiphaga DSM 21508

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_057508105.1 ABB28_RS07810 dihydrolipoyl dehydrogenase

Query= BRENDA::Q0KBV8
         (594 letters)



>NCBI__GCF_001431535.1:WP_057508105.1
          Length = 603

 Score =  689 bits (1779), Expect = 0.0
 Identities = 372/615 (60%), Positives = 452/615 (73%), Gaps = 33/615 (5%)

Query: 1   MSVIEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVK 60
           M+ IEVKVPDIGD+  V VIE+LV  GDTV+ +Q L+ LESDKA+++VPSSAAG V EVK
Sbjct: 1   MATIEVKVPDIGDYSDVPVIELLVAVGDTVKKDQGLLTLESDKATLEVPSSAAGVVKEVK 60

Query: 61  VKVGDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAP-----------APAPA 109
           VK+GD + +GAV+  +EA+   AAPA     APA+A AP AAAP           APA  
Sbjct: 61  VKLGDTLSEGAVVVLLEAEGEGAAPA-----APAKAAAPVAAAPNSKPPVTPSHRAPAEP 115

Query: 110 AA-----SHSGGADIQCEMLVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGC 164
           AA     S    ADI+C M+VLG+GPGGY+AAFRAAD+G++TV+VERY++LGGVCLNVGC
Sbjct: 116 AAPKPALSSGKAADIECAMVVLGSGPGGYTAAFRAADVGLDTVIVERYASLGGVCLNVGC 175

Query: 165 IPSKALLHNAAVIDEAKALAAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKV 224
           IPSKALLH AAVIDE       G+ FG  KI LD LR YK +VVG+LT GLAGMAK RKV
Sbjct: 176 IPSKALLHAAAVIDEVAHAGDFGVEFGAPKITLDKLRQYKEKVVGQLTKGLAGMAKQRKV 235

Query: 225 QVVRGIGNFLDPHHMEVELTEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIP-EDPRI 283
           + V+G+G F+  + +E+   +G  +       ++RF++ IIAAGSQAVKLP  P +DPR+
Sbjct: 236 RSVQGVGRFVSANELEITAEDGSTQ-------LLRFQQCIIAAGSQAVKLPNFPWDDPRV 288

Query: 284 VDSTGALELPEVPNKMLVIGGGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVW 343
           +DST ALEL +VP  +LV+GGGIIGLEMATVY+ LG+ + VVE +D LM GAD+DLVK  
Sbjct: 289 MDSTDALELADVPGSLLVVGGGIIGLEMATVYAALGSKVTVVEFMDQLMPGADKDLVKPL 348

Query: 344 EKKNKDRFGKVMLKTKTVGVEAKPDGIYVKFEGEA---APAEPQ-RYDLVLVSVGRSPNG 399
             + K +   V LKTK  GV A   G+ V FE  A    PA PQ  +D VLV+VGRSPNG
Sbjct: 349 ADRLKKQGVDVHLKTKASGVTADAKGVTVTFEAAAEGETPALPQGTFDRVLVAVGRSPNG 408

Query: 400 KRISAEKAGVAVSERGFINVDKQMRTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHG 459
            +I AE AGV VS+RGFI VD+QMRTNVPHIFAIGDIVG PMLAHKA HE  +AAE A G
Sbjct: 409 AKIGAENAGVQVSDRGFIPVDRQMRTNVPHIFAIGDIVGNPMLAHKATHEGKLAAEVAAG 468

Query: 460 EKAYFDAKQIPSVAFTDPEVAWAGLTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFT 519
            K  + A+ IPSVA+T+PE+AW G+TE E K KG+K     FPWAASGRAI  GR EGFT
Sbjct: 469 HKKEWVARVIPSVAYTNPEIAWVGVTETEAKAKGLKVGVAKFPWAASGRAIGIGRTEGFT 528

Query: 520 KLIFDEETHRVIGGGIVGTHAGDLISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAE 579
           KLIFDEETHR+IGG IVG HAGDL++E+ LAIEMGA+A DIG TIH HPTL ES+ MA+E
Sbjct: 529 KLIFDEETHRIIGGAIVGVHAGDLLAEIGLAIEMGAEAEDIGHTIHAHPTLSESVAMASE 588

Query: 580 IYEGTCTDVPPPRKR 594
           IY+GT TD+  P+K+
Sbjct: 589 IYDGTITDLYMPKKK 603


Lambda     K      H
   0.316    0.134    0.387 

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: 974
Number of extensions: 41
Number of successful extensions: 7
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: 594
Length of database: 603
Length adjustment: 37
Effective length of query: 557
Effective length of database: 566
Effective search space:   315262
Effective search space used:   315262
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: 53 (25.0 bits)

Align candidate WP_057508105.1 ABB28_RS07810 (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.16555.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-154  501.0   5.0     2e-154  500.6   5.0    1.1  1  lcl|NCBI__GCF_001431535.1:WP_057508105.1  ABB28_RS07810 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508105.1  ABB28_RS07810 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.6   5.0    2e-154    2e-154       3     452 ..     133     588 ..     131     595 .. 0.95

  Alignments for each domain:
  == domain 1  score: 500.6 bits;  conditional E-value: 2e-154
                                 TIGR01350   3 dvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelkeakelgiev 70 
                                                +vv+G+GpgGY+aA raa  gl +++ve+  +lGG+ClnvGCiP+KalL++a v++e+ +a ++g+e 
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 133 AMVVLGSGPGGYTAAFRAADVGLDTVIVERyASLGGVCLNVGCIPSKALLHAAAVIDEVAHAGDFGVEF 201
                                               589***************************99************************************* PP

                                 TIGR01350  71 envkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiA 138
                                                  k+ l+kl + kekvv +l++G++++ k+ kv +++G +++++++e+e+++e+++ + l+++++iiA
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 202 GAPKITLDKLRQYKEKVVGQLTKGLAGMAKQRKVRSVQGVGRFVSANELEITAEDGStQLLRFQQCIIA 270
                                               *****************************************************99887999******** PP

                                 TIGR01350 139 tGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilp 207
                                                Gs+  +lp  +  d  +v++s++alel  vp sl++vGgG+iG+E+a+++a lG+kvtv+e++d+++p
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 271 AGSQAVKLPN-FPWDDPRVMDSTDALELADVPGSLLVVGGGIIGLEMATVYAALGSKVTVVEFMDQLMP 338
                                               **********.999999**************************************************** PP

                                 TIGR01350 208 aldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk......evetleaekvLvavGrkpn 270
                                                 d+++ k l+++lkk+gv+++ ++k + v+++++ v+v+ +           + + ++vLvavGr+pn
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 339 GADKDLVKPLADRLKKQGVDVHLKTKASGVTADAKGVTVTFEAAaegetpALPQGTFDRVLVAVGRSPN 407
                                               ********************************9999995544432120122345588************ PP

                                 TIGR01350 271 leelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidy 339
                                                 ++g e+ gv++ +rg+i+vd+++rtnvp+i+aiGD++g++mLAh+A++eg +aae +ag++k e  +
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 408 GAKIGAENAGVQVSDRGFIPVDRQMRTNVPHIFAIGDIVGNPMLAHKATHEGKLAAEVAAGHKK-EWVA 475
                                               *************************************************************776.999* PP

                                 TIGR01350 340 kavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahi 408
                                               +++Psv yt+Pe+a vG+te++ak++g +v v+kfp aa+g+a+ ++ t+Gf k+i+d++t++i+G  i
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 476 RVIPSVAYTNPEIAWVGVTETEAKAKGLKVGVAKFPWAASGRAIGIGRTEGFTKLIFDEETHRIIGGAI 544
                                               ********************************************************************* PP

                                 TIGR01350 409 vgaeaseliselalaveleltveelaktihpHPtlsEaikeaal 452
                                               vg +a +l++e+ la+e+++++e++ +tih+HPtlsE ++ a +
  lcl|NCBI__GCF_001431535.1:WP_057508105.1 545 VGVHAGDLLAEIGLAIEMGAEAEDIGHTIHAHPTLSESVAMASE 588
                                               *************************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (603 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: 00:00:00.03
# Mc/sec: 8.37
//
[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