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_011653804.1 RL_RS22840 dihydrolipoyl dehydrogenase

Query= BRENDA::Q9M5K2
         (507 letters)



>NCBI__GCF_000009265.1:WP_011653804.1
          Length = 468

 Score =  548 bits (1413), Expect = e-160
 Identities = 266/465 (57%), Positives = 349/465 (75%), Gaps = 2/465 (0%)

Query: 45  DVVIIGGGPGGYVAAIKAAQLGLKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYHEAK 104
           DV+IIG GPGGYV A+KAAQLGLK   +EKR   GGTCLNVGCIPSKALLH+S M+H+A 
Sbjct: 4   DVIIIGTGPGGYVCAVKAAQLGLKVAVVEKRATYGGTCLNVGCIPSKALLHASEMFHQAG 63

Query: 105 HVFANHGVKVSSVEVDLPAMLAQKDTAVKNLTRGVEGLFKKNKVNYVKGYGKFLSPSEVS 164
           H  +  G+ V +  ++L  M+A KD  VK+   GV  LFKKNK++  +G GK +S  +VS
Sbjct: 64  HGMSALGIDVPAPTLNLGNMMAHKDATVKSNVDGVAFLFKKNKIDAFQGTGKIVSAGKVS 123

Query: 165 VDTIDGENVVVKGKHIIVATGSDVKSLPGIT--IDEKKIVSSTGALSLTEIPKKLIVIGA 222
           V   DG+   ++GK+I++ATGSDV  +PG+   IDEK I+SSTG ++L ++P+ LIV+G 
Sbjct: 124 VTADDGKVQDIEGKNIVIATGSDVAGIPGVQVEIDEKTIISSTGGIALEKVPETLIVVGG 183

Query: 223 GYIGLEMGSVWGRLGSEVTVVEFAADIVPAMDGEIRKQFQRSLEKQKMKFMLKTKVVGVD 282
           G IGLE+GSVW RLG++VTVVE+   I+  MDGE+ KQFQR L KQ + F L  KV GV+
Sbjct: 184 GVIGLELGSVWSRLGAKVTVVEYLDTILGGMDGEVSKQFQRMLAKQGIDFNLSAKVTGVE 243

Query: 283 SSGDGVKLIVEPAEGGEQTTLEADVVLVSAGRTPFTSGLDLEKIGVETDKGGRILVNERF 342
            +  G K+  EP +GG++ TL+A+VVL++ GR P+T+GL LE+ GV  D  GR+ ++  +
Sbjct: 244 KADKGAKVTFEPVKGGDKVTLDAEVVLIATGRKPYTAGLGLEEAGVTLDNRGRVEIDGHY 303

Query: 343 STNVSGVYAIGDVIPGPMLAHKAEEDGVACVEFIAGKHGHVDYDKVPGVVYTYPEVASVG 402
            TNV G+YAIGDV+ GPMLAHKAE++GVA  E +AG+HGHV+Y+ +P VVYT PE+ASVG
Sbjct: 304 KTNVDGIYAIGDVVKGPMLAHKAEDEGVALAEILAGQHGHVNYEVIPSVVYTQPEIASVG 363

Query: 403 KTEEQLKKEGVSYNVGKFPFMANSRAKAIDTAEGMVKILADKETDKILGVHIMSPNAGEL 462
           KTEE+LK  GV+Y VGKFPF AN RA+A+   +G VKILADKETD++LG HI+   AGE+
Sbjct: 364 KTEEELKAAGVAYKVGKFPFTANGRARAMLATDGFVKILADKETDRVLGGHIVGFGAGEM 423

Query: 463 IHEAVLAINYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHM 507
           IHE  + + +  SSED+ R CHAHPTMSEA+KEAA+AT+ KPIHM
Sbjct: 424 IHEIAVLMEFGGSSEDLGRTCHAHPTMSEAVKEAALATFFKPIHM 468


Lambda     K      H
   0.315    0.134    0.376 

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: 698
Number of extensions: 30
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: 507
Length of database: 468
Length adjustment: 34
Effective length of query: 473
Effective length of database: 434
Effective search space:   205282
Effective search space used:   205282
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: 52 (24.6 bits)

Align candidate WP_011653804.1 RL_RS22840 (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.22841.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-180  586.7  15.0   1.7e-180  586.6  15.0    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011653804.1  RL_RS22840 dihydrolipoyl dehydro


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011653804.1  RL_RS22840 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  586.6  15.0  1.7e-180  1.7e-180       1     461 []       2     468 .]       2     468 .] 0.97

  Alignments for each domain:
  == domain 1  score: 586.6 bits;  conditional E-value: 1.7e-180
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelg 67 
                                               +ydv++iG+GpgGYv+A++aaqlglkva+vek  ++GGtClnvGCiP+KalL+++e+++++ + ++ lg
  lcl|NCBI__GCF_000009265.1:WP_011653804.1   2 SYDVIIIGTGPGGYVCAVKAAQLGLKVAVVEKrATYGGTCLNVGCIPSKALLHASEMFHQAGHgMSALG 70 
                                               59******************************899********************************** PP

                                 TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakni 135
                                               i+v   +l+l +++++k+++vk+ v+Gv++L+kknk++ ++G++k++++++v+v++++++ + +e kni
  lcl|NCBI__GCF_000009265.1:WP_011653804.1  71 IDVPAPTLNLGNMMAHKDATVKSNVDGVAFLFKKNKIDAFQGTGKIVSAGKVSVTADDGKvQDIEGKNI 139
                                               ********************************************************999889******* PP

                                 TIGR01350 136 iiAtGseprelplk.leedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielld 203
                                               +iAtGs+++ +p+  +e dek++i+s++ ++l++vpe+l++vGgGviG+E++s++++lG+kvtv+e+ld
  lcl|NCBI__GCF_000009265.1:WP_011653804.1 140 VIATGSDVAGIPGVqVEIDEKTIISSTGGIALEKVPETLIVVGGGVIGLELGSVWSRLGAKVTVVEYLD 208
                                               *************99****************************************************** PP

                                 TIGR01350 204 rilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkp 269
                                               +il  +d evsk+ +++l k+g+++  +akvt vek ++  +  +e  k+ ++ tl+ae vL+a Grkp
  lcl|NCBI__GCF_000009265.1:WP_011653804.1 209 TILGGMDGEVSKQFQRMLAKQGIDFNLSAKVTGVEKADKGAKvtFEPVKGgDKVTLDAEVVLIATGRKP 277
                                               ********************************8887766544236666666999*************** PP

                                 TIGR01350 270 nleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseid 338
                                                + +lgle+ gv+ld+rg++++d +++tnv+giyaiGDv++++mLAh+A++egv  ae +ag++  +++
  lcl|NCBI__GCF_000009265.1:WP_011653804.1 278 YTAGLGLEEAGVTLDNRGRVEIDGHYKTNVDGIYAIGDVVKGPMLAHKAEDEGVALAEILAGQHG-HVN 345
                                               **************************************************************998.9** PP

                                 TIGR01350 339 ykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGah 407
                                               y+++Psv+yt+Pe+asvG+tee++k++g+++kvgkfpf+ang+a+a+  tdGfvk+++dk+t+++lG h
  lcl|NCBI__GCF_000009265.1:WP_011653804.1 346 YEVIPSVVYTQPEIASVGKTEEELKAAGVAYKVGKFPFTANGRARAMLATDGFVKILADKETDRVLGGH 414
                                               ********************************************************************* PP

                                 TIGR01350 408 ivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               ivg  a e+i+e+a+++e+++++e+l +t+h+HPt+sEa+keaala++ k+ih+
  lcl|NCBI__GCF_000009265.1:WP_011653804.1 415 IVGFGAGEMIHEIAVLMEFGGSSEDLGRTCHAHPTMSEAVKEAALATFFKPIHM 468
                                               *****************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 6.87
//
[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