Alignments for a candidate for lpd in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Rhizobium leguminosarum 3841

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011651835.1 RL_RS11630 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000009265.1:WP_011651835.1
          Length = 482

 Score =  509 bits (1311), Expect = e-149
 Identities = 256/483 (53%), Positives = 336/483 (69%), Gaps = 20/483 (4%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA+ +D+I++G GPGGYVAAIRA+QL LK A+VER H+GGICLNWGCIPTK+LLRSAEV 
Sbjct: 1   MAESYDVIIIGSGPGGYVAAIRASQLGLKTAIVEREHMGGICLNWGCIPTKALLRSAEVL 60

Query: 61  HEMQNAEAYGLT---SFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLT 117
               + + +GL    + KPD     ++ RSR V+ RL +GV  L++KNK+++I G  ++T
Sbjct: 61  DHANHFKDFGLVLEGTVKPD--AKAVVGRSRAVSARLNAGVGFLMKKNKIDIIWGEAKIT 118

Query: 118 GNQQMLV---------------ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWT 162
              +++V               +  +  E    AK IIIATGAR R LP +  DGK IWT
Sbjct: 119 KPGEIVVGKSSKPVVEPQHPLPKNVKSGEGTYTAKHIIIATGARPRALPGIEPDGKLIWT 178

Query: 163 YHHALKPPAMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAK 222
           Y  ALKP  +PK L+V+GSGAIGIEFASFY   G +V++VE  P I+P+EDAE++A   K
Sbjct: 179 YFEALKPDLLPKSLIVMGSGAIGIEFASFYRSMGVDVTVVEVMPTIMPVEDAEITAIARK 238

Query: 223 AFKKRGIRILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLD 282
             +KRG++I T + +  +      VTA +  ADGKV +      I A+GV  N+EN+GL+
Sbjct: 239 QLEKRGLKIFTSAKVSKVDKATNSVTAHVETADGKVQQITADRLISAVGVQGNIENLGLE 298

Query: 283 KLGIKLDRGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPL 342
            LG+K DRG + +DG+G+TNV  ++AIGDVAG P LAHKA H+GV+  E IAG  +VHP 
Sbjct: 299 ALGVKTDRGCVVIDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVVCVEKIAGLPNVHPT 358

Query: 343 NTQNIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFD 402
           +   +PGCTY  PQVASVG+TE KA++QG ++++G F F ANGKAIA G   G VK +FD
Sbjct: 359 DKGKVPGCTYCNPQVASVGITEAKAKEQGRDIRVGRFSFAANGKAIALGEDQGMVKVIFD 418

Query: 403 ADSGALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGR 462
             +G LLGAHMVGAEVTE+IQG+ VA  LETTE E+M TIFPHPT+SE+M E+VL AYGR
Sbjct: 419 KKTGELLGAHMVGAEVTELIQGFVVAMNLETTEEELMHTIFPHPTVSESMKEAVLDAYGR 478

Query: 463 ALH 465
            L+
Sbjct: 479 VLN 481


Lambda     K      H
   0.319    0.135    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: 677
Number of extensions: 30
Number of successful extensions: 3
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: 466
Length of database: 482
Length adjustment: 33
Effective length of query: 433
Effective length of database: 449
Effective search space:   194417
Effective search space used:   194417
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011651835.1 RL_RS11630 (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.29192.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-180  584.3   8.1     1e-179  584.0   8.1    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011651835.1  RL_RS11630 dihydrolipoyl dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011651835.1  RL_RS11630 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.0   8.1    1e-179    1e-179       1     459 [.       4     480 ..       4     482 .] 0.98

  Alignments for each domain:
  == domain 1  score: 584.0 bits;  conditional E-value: 1e-179
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                               +ydv++iG+GpgGYvaAira+qlglk+a+ve+e++GG+Cln+GCiPtKalL+saev+++++++k++g+ 
  lcl|NCBI__GCF_000009265.1:WP_011651835.1   4 SYDVIIIGSGPGGYVAAIRASQLGLKTAIVEREHMGGICLNWGCIPTKALLRSAEVLDHANHFKDFGLV 72 
                                               59******************************************************************* PP

                                 TIGR01350  70 ven.vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.......... 127
                                               +e+ vk d ++++ r+++v+ +l++Gv +L+kknk++ i+Geak+++++e+ v k++k           
  lcl|NCBI__GCF_000009265.1:WP_011651835.1  73 LEGtVKPDAKAVVGRSRAVSARLNAGVGFLMKKNKIDIIWGEAKITKPGEIVVGKSSKPvvepqhplpk 141
                                               9999*************************************************999876899999***9 PP

                                 TIGR01350 128 ......kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifa 190
                                                      +++ak+iiiAtG++pr+lp+ +e d+k+++t+ eal+ + +p+sl+++G+G+iG+Efas+++
  lcl|NCBI__GCF_000009265.1:WP_011651835.1 142 nvksgeGTYTAKHIIIATGARPRALPG-IEPDGKLIWTYFEALKPDLLPKSLIVMGSGAIGIEFASFYR 209
                                               9988877899*****************.***************************************** PP

                                 TIGR01350 191 klGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkkevetle 257
                                               ++Gv+vtv+e++++i+p++dae++ +++k+l+k+g+ki t+akv++v k  ++v+  ve+ +++v++++
  lcl|NCBI__GCF_000009265.1:WP_011651835.1 210 SMGVDVTVVEVMPTIMPVEDAEITAIARKQLEKRGLKIFTSAKVSKVDKATNSVTahVETADGKVQQIT 278
                                               *******************************************************888888889***** PP

                                 TIGR01350 258 aekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaa 326
                                               a++++ avG++ n+e+lgle+lgv++d+ g++++d + +tnv+giyaiGDv+g++mLAh+A++egvv++
  lcl|NCBI__GCF_000009265.1:WP_011651835.1 279 ADRLISAVGVQGNIENLGLEALGVKTDR-GCVVIDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVVCV 346
                                               *************************776.**************************************** PP

                                 TIGR01350 327 ekiagkeks.eidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkv 394
                                               ekiag  +   +d+ +vP ++y++P+vasvG+te++ake+g +++vg+f+faangka+al+e++G+vkv
  lcl|NCBI__GCF_000009265.1:WP_011651835.1 347 EKIAGLPNVhPTDKGKVPGCTYCNPQVASVGITEAKAKEQGRDIRVGRFSFAANGKAIALGEDQGMVKV 415
                                               *****9887799********************************************************* PP

                                 TIGR01350 395 ivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkai 459
                                               i+dkktge+lGah+vgae++eli+ +++a++le+t+eel++ti+pHPt+sE +kea+l+a+g+ +
  lcl|NCBI__GCF_000009265.1:WP_011651835.1 416 IFDKKTGELLGAHMVGAEVTELIQGFVVAMNLETTEEELMHTIFPHPTVSESMKEAVLDAYGRVL 480
                                               ************************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (482 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: 8.10
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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