Alignments for a candidate for lpd in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Belnapia rosea CPCC 100156

Align Dihydrolipoyl dehydrogenase, mitochondrial; Dihydrolipoamide dehydrogenase; Glycine cleavage system L protein; Pyruvate dehydrogenase complex E3 subunit; E3; PDC-E3; EC 1.8.1.4 (characterized)
to candidate WP_090664006.1 BLR02_RS16900 dihydrolipoyl dehydrogenase

Query= SwissProt::P31023
         (501 letters)



>NCBI__GCF_900101615.1:WP_090664006.1
          Length = 463

 Score =  538 bits (1385), Expect = e-157
 Identities = 261/466 (56%), Positives = 348/466 (74%), Gaps = 5/466 (1%)

Query: 36  DENDVVIIGGGPGGYVAAIKAAQLGFKTTCIEKRGALGGTCLNVGCIPSKALLHSSHMYH 95
           D  D+++IG GPGGYV AI+AAQLG KT C+EKR  LGGTCLN+GCIPSKALL SS  + 
Sbjct: 3   DSFDLIVIGSGPGGYVCAIRAAQLGLKTACVEKRATLGGTCLNIGCIPSKALLQSSENFE 62

Query: 96  EAKHSFANHGVKVSNVEIDLAAMMGQKDKAVSNLTRGIEGLFKKNKVTYVKGYGKFVSPS 155
           EA H  A+HGV V  V++DLA M  +K + VS   +G+E LF+KNKVT++KG G+  +P 
Sbjct: 63  EAAHKLADHGVIVDGVKLDLAKMQARKGEVVSANVKGVEFLFRKNKVTWLKGAGRITAPG 122

Query: 156 EISVDTIEGENTVVKGKHIIIATGSDVKSLPGVTIDEKKIVSSTGALALSEIPKKLVVIG 215
           ++ V+   GE    K   I+IATGSD   L GV +DEK++V+STGAL L ++P  LVVIG
Sbjct: 123 QVEVN---GETYSTKA--IVIATGSDSTPLRGVEVDEKRVVTSTGALELDKVPGHLVVIG 177

Query: 216 AGYIGLEMGSVWGRIGSEVTVVEFASEIVPTMDAEIRKQFQRSLEKQGMKFKLKTKVVGV 275
            G IGLE+GSVW R+G++VTV+EF   ++P MDAE+ KQ +R+  KQGMKF+LK+KV   
Sbjct: 178 GGVIGLELGSVWKRLGAQVTVIEFLDRLIPGMDAELAKQAERTFGKQGMKFRLKSKVTAA 237

Query: 276 DTSGDGVKLTVEPSAGGEQTIIEADVVLVSAGRTPFTSGLNLDKIGVETDKLGRILVNER 335
               DGV LTVEP+AGG    I+ADVVL++ GR P+  GL L ++GV  D+ GR++ +  
Sbjct: 238 RQDADGVTLTVEPAAGGTAEEIKADVVLLAIGRRPYIEGLGLQEVGVALDERGRVVTDGH 297

Query: 336 FSTNVSGVYAIGDVIPGPMLAHKAEEDGVACVEYLAGKVGHVDYDKVPGVVYTNPEVASV 395
           F+TN+ G+YAIGD I G MLAHKAEE+GVA  E LAG+ GHV+Y  +PGVVYT PE+ASV
Sbjct: 298 FATNIPGIYAIGDCIAGAMLAHKAEEEGVAVAEILAGQAGHVNYGAIPGVVYTWPEIASV 357

Query: 396 GKTEEQVKETGVEYRVGKFPFMANSRAKAIDNAEGLVKIIAEKETDKILGVHIMAPNAGE 455
           G TEE++K  G+ Y+VGKFPF AN RA+A+++ EG VKI+A+ ++DK+LG HI+ P+AG 
Sbjct: 358 GATEEELKAQGIAYKVGKFPFTANGRARAMNDTEGFVKILADAKSDKVLGAHIIGPDAGT 417

Query: 456 LIHEAAIALQYDASSEDIARVCHAHPTMSEAIKEAAMATYDKPIHI 501
           LI E A+A+++ AS+ED+AR  HAHPT++EA+KEAA+A   + +HI
Sbjct: 418 LIAEMALAIEFGASAEDVARTSHAHPTLNEAVKEAALAADGRALHI 463


Lambda     K      H
   0.315    0.133    0.370 

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: 633
Number of extensions: 26
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: 501
Length of database: 463
Length adjustment: 34
Effective length of query: 467
Effective length of database: 429
Effective search space:   200343
Effective search space used:   200343
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: 42 (22.0 bits)
S2: 52 (24.6 bits)

Align candidate WP_090664006.1 BLR02_RS16900 (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.1236935.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-179  581.7   8.2   5.5e-179  581.6   8.2    1.0  1  NCBI__GCF_900101615.1:WP_090664006.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900101615.1:WP_090664006.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.6   8.2  5.5e-179  5.5e-179       2     461 .]       5     463 .]       4     463 .] 0.98

  Alignments for each domain:
  == domain 1  score: 581.6 bits;  conditional E-value: 5.5e-179
                             TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akelgieven 72 
                                           +d++viG+GpgGYv+Airaaqlglk+a+vek  +lGGtCln GCiP+KalL+s+e++ee+ + ++++g+ v++
  NCBI__GCF_900101615.1:WP_090664006.1   5 FDLIVIGSGPGGYVCAIRAAQLGLKTACVEKrATLGGTCLNIGCIPSKALLQSSENFEEAAHkLADHGVIVDG 77 
                                           8******************************899*************************************** PP

                             TIGR01350  73 vkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGsepre 145
                                           vkldl+k+++rk +vv+  v+Gv++L++knkv+ +kG ++++ +++vev++e+    +++k+i+iAtGs+ + 
  NCBI__GCF_900101615.1:WP_090664006.1  78 VKLDLAKMQARKGEVVSANVKGVEFLFRKNKVTWLKGAGRITAPGQVEVNGET----YSTKAIVIATGSDSTP 146
                                           ***************************************************98....56************** PP

                             TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218
                                           l++ +e+dek+v+ts++alel++vp +lv++GgGviG+E++s++++lG++vtvie+ldr++p +dae++k+++
  NCBI__GCF_900101615.1:WP_090664006.1 147 LRG-VEVDEKRVVTSTGALELDKVPGHLVVIGGGVIGLELGSVWKRLGAQVTVIEFLDRLIPGMDAELAKQAE 218
                                           ***.********************************************************************* PP

                             TIGR01350 219 kklkkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleelgleklgvelderga 288
                                           +++ k+g+k+  ++kvt+ ++++d v+  ve   + ++e+++a+ vL+a+Gr+p +e+lgl+++gv lderg+
  NCBI__GCF_900101615.1:WP_090664006.1 219 RTFGKQGMKFRLKSKVTAARQDADGVTltVEPAAGgTAEEIKADVVLLAIGRRPYIEGLGLQEVGVALDERGR 291
                                           **************************966555555589*********************************** PP

                             TIGR01350 289 ikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeq 361
                                           +++d ++ tn+pgiyaiGD+i+++mLAh+A++egv +ae +ag++  +++y a+P v+yt Pe+asvG tee+
  NCBI__GCF_900101615.1:WP_090664006.1 292 VVTDGHFATNIPGIYAIGDCIAGAMLAHKAEEEGVAVAEILAGQAG-HVNYGAIPGVVYTWPEIASVGATEEE 363
                                           *******************************************998.9************************* PP

                             TIGR01350 362 akeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434
                                           +k++gi++kvgkfpf+ang+a+a+++t+Gfvk+++d k++++lGahi+g++a  li+e+ala+e+++++e++a
  NCBI__GCF_900101615.1:WP_090664006.1 364 LKAQGIAYKVGKFPFTANGRARAMNDTEGFVKILADAKSDKVLGAHIIGPDAGTLIAEMALAIEFGASAEDVA 436
                                           ************************************************************************* PP

                             TIGR01350 435 ktihpHPtlsEaikeaalaalgkaihv 461
                                           +t h+HPtl+Ea+keaalaa g+a+h+
  NCBI__GCF_900101615.1:WP_090664006.1 437 RTSHAHPTLNEAVKEAALAADGRALHI 463
                                           ***********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (463 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 20.61
//
[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 2024 update 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