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 (EC 1.8.1.4) (characterized)
to candidate WP_090659972.1 BLR02_RS01950 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_900101615.1:WP_090659972.1
          Length = 467

 Score =  551 bits (1420), Expect = e-161
 Identities = 273/462 (59%), Positives = 347/462 (75%), Gaps = 1/462 (0%)

Query: 4   HFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEM 63
           +FDLIVLGGGPGGYVAAIRA QL +K ALVER HLGGICLNWGCIPTK+LLRS+E+ H +
Sbjct: 6   NFDLIVLGGGPGGYVAAIRATQLGMKTALVEREHLGGICLNWGCIPTKALLRSSEINHLL 65

Query: 64  QNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQML 123
              +AYG  +    FD+ KI+ RSR VA +L+ GVK LLRKNKV V  G G+L G  +M 
Sbjct: 66  HTLDAYGFAADNIRFDIGKIVKRSRAVANQLSGGVKHLLRKNKVTVFDGQGRLAGKGRMS 125

Query: 124 VETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGA 183
           V         L AK II+ATGARAR LP + +DGK +W+Y  A+ PP+MPK L+VIGSGA
Sbjct: 126 VTKDGKPVAELAAKHIILATGARARTLPGLEADGKLVWSYKEAMVPPSMPKSLIVIGSGA 185

Query: 184 IGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPD 243
           IG EFASFY + GA+V++VE   ++LP+EDAE+SA+V KAF+K+G+ ILT + +Q L   
Sbjct: 186 IGSEFASFYLNLGAKVTLVEVMDRVLPVEDAEISAFVRKAFEKQGMTILTGAKVQGLRKG 245

Query: 244 DEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNV 303
           ++ VTA I  A GKV +      I A+G+V NVE+IGL+  G+K++R  + VD + RT  
Sbjct: 246 EDSVTAVIE-AGGKVQEVTADRVISAVGIVGNVEDIGLEGTGVKVERAHVVVDQYCRTGE 304

Query: 304 DHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLT 363
             ++AIGD+ GAP LAHKASH+G++  E IAG   VHP+   NIPGCTY RPQVASVGLT
Sbjct: 305 PGIYAIGDLTGAPWLAHKASHEGILCVETIAGVKGVHPMEVLNIPGCTYCRPQVASVGLT 364

Query: 364 EEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQ 423
           EE A++ G+ +++G FPFI NGKAIA G  +G +KT+FDA +G LLGAHMVG EVTEMIQ
Sbjct: 365 EEAAKKAGHELRVGRFPFIGNGKAIAMGEPEGLIKTIFDAKTGELLGAHMVGPEVTEMIQ 424

Query: 424 GYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           GYT+A+T+ETTE E++ +IFPHPT+SEAMHE+VL AYGR +H
Sbjct: 425 GYTIAKTMETTEEELIHSIFPHPTISEAMHEAVLDAYGRVIH 466


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: 655
Number of extensions: 27
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: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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_090659972.1 BLR02_RS01950 (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.2599811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-173  563.8   4.9   1.6e-173  563.6   4.9    1.0  1  NCBI__GCF_900101615.1:WP_090659972.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900101615.1:WP_090659972.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.6   4.9  1.6e-173  1.6e-173       1     461 []       6     467 .]       6     467 .] 0.98

  Alignments for each domain:
  == domain 1  score: 563.6 bits;  conditional E-value: 1.6e-173
                             TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenv 73 
                                           ++d++v+GgGpgGYvaAira qlg+k+alve+e+lGG+Cln+GCiPtKalL+s+e+ + l++++ +g+ ++n+
  NCBI__GCF_900101615.1:WP_090659972.1   6 NFDLIVLGGGPGGYVAAIRATQLGMKTALVEREHLGGICLNWGCIPTKALLRSSEINHLLHTLDAYGFAADNI 78 
                                           69********************************************************9999*********** PP

                             TIGR01350  74 kldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGsepre 145
                                           ++d+ k+++r+++v ++l+gGvk+Ll+knkv+v+ G+++l +k++++v+k+ k   +l ak+ii+AtG++ r+
  NCBI__GCF_900101615.1:WP_090659972.1  79 RFDIGKIVKRSRAVANQLSGGVKHLLRKNKVTVFDGQGRLAGKGRMSVTKDGKPvAELAAKHIILATGARART 151
                                           *************************************************9987678999************** PP

                             TIGR01350 146 lplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlk 218
                                           lp+ le+d+k+v++++ea+  +++p+sl+++G+G+iG Efas++ +lG+kvt++e++dr+lp++dae+s +++
  NCBI__GCF_900101615.1:WP_090659972.1 152 LPG-LEADGKLVWSYKEAMVPPSMPKSLIVIGSGAIGSEFASFYLNLGAKVTLVEVMDRVLPVEDAEISAFVR 223
                                           ***.********************************************************************* PP

                             TIGR01350 219 kklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaik 290
                                           k+++k+g++ilt+akv+ ++k ed+v++ ++ + +v++++a++v+ avG   n+e++gle +gv++++   ++
  NCBI__GCF_900101615.1:WP_090659972.1 224 KAFEKQGMTILTGAKVQGLRKGEDSVTAVIEAGgKVQEVTADRVISAVGIVGNVEDIGLEGTGVKVER-AHVV 295
                                           ***************************54444448******************************988.77** PP

                             TIGR01350 291 vdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePevasvGlteeqa 362
                                           vd+++rt  pgiyaiGD++g + LAh+As+eg++++e+iag +    ++   +P ++y++P+vasvGltee a
  NCBI__GCF_900101615.1:WP_090659972.1 296 VDQYCRTGEPGIYAIGDLTGAPWLAHKASHEGILCVETIAGVKGVhPMEVLNIPGCTYCRPQVASVGLTEEAA 368
                                           *****************************************988779************************** PP

                             TIGR01350 363 keegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelak 435
                                           k++g+e++vg+fpf  ngka+a++e +G++k+i+d ktge+lGah+vg+e++e+i+  ++a ++e+t+eel +
  NCBI__GCF_900101615.1:WP_090659972.1 369 KKAGHELRVGRFPFIGNGKAIAMGEPEGLIKTIFDAKTGELLGAHMVGPEVTEMIQGYTIAKTMETTEEELIH 441
                                           ************************************************************************* PP

                             TIGR01350 436 tihpHPtlsEaikeaalaalgkaihv 461
                                           +i+pHPt+sEa++ea+l+a+g+ ih+
  NCBI__GCF_900101615.1:WP_090659972.1 442 SIFPHPTISEAMHEAVLDAYGRVIHM 467
                                           ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (467 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 30.04
//
[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