Alignments for a candidate for lpd in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Sphingomonas koreensis DSMZ 15582

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Ga0059261_3715 Ga0059261_3715 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Korea:Ga0059261_3715
          Length = 466

 Score =  580 bits (1496), Expect = e-170
 Identities = 289/466 (62%), Positives = 362/466 (77%), Gaps = 2/466 (0%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA+ +D+IVLG GPGGYVAAIRA+QL LK A+VER  LGGICLNWGCIPTK+LLRSAE++
Sbjct: 1   MAESYDVIVLGSGPGGYVAAIRASQLGLKTAIVERELLGGICLNWGCIPTKALLRSAEIF 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
           H MQ+A+ YGL + K   DL+ ++ RSR VA +L  GV  L++KNKV V  G G+LTG  
Sbjct: 61  HFMQHAKDYGLAAEKITADLEAVVKRSRGVAKQLNQGVTHLMKKNKVAVHFGTGKLTGKG 120

Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180
           ++ V   +G+   L AK+II+ATGARAR LPN+ +DG  +WTY HA+ P  MPKKLLVIG
Sbjct: 121 KLSVTAEDGKVTELTAKNIILATGARARDLPNLPADGNKVWTYRHAMTPKEMPKKLLVIG 180

Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240
           SGAIGIEFASFY D G+EV++VE   +I+P+EDA++SA++ KA KK+G+ I+T + +  +
Sbjct: 181 SGAIGIEFASFYNDMGSEVTVVEMLDRIVPVEDADISAHLEKALKKQGMTIMTGAKVDKI 240

Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKL-DRGFIAVDGFG 299
             D  GV A I G DGK    +FSH IVAIG+V N  +IGL +LG+ + DRGF+      
Sbjct: 241 AADATGVKATITGKDGKAVDGQFSHVIVAIGIVPNTADIGLKELGVDVDDRGFLRTGPDC 300

Query: 300 RTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVAS 359
           +TN+D ++AIGD+   P LAHKASH+GVIAAEAIAG  H H ++ +NIPGCTY  PQ+AS
Sbjct: 301 KTNIDGLYAIGDITAPPWLAHKASHEGVIAAEAIAG-KHPHAMDPRNIPGCTYCHPQIAS 359

Query: 360 VGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVT 419
           VGLTE KA++ GY VK+GNFPFI NGKAIA G  +GFVKTVFDA +G LLGAHM+GAEVT
Sbjct: 360 VGLTEAKAKEAGYEVKVGNFPFIGNGKAIALGEPEGFVKTVFDAKTGELLGAHMIGAEVT 419

Query: 420 EMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           EMIQGYT+ +TLETTEAE+MET+FPHPT+SE MHE+VLAAYGR LH
Sbjct: 420 EMIQGYTIGKTLETTEAELMETVFPHPTISETMHEAVLAAYGRQLH 465


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: 721
Number of extensions: 28
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: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 Ga0059261_3715 Ga0059261_3715 (dihydrolipoamide 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.13996.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.9e-177  576.5   6.3   2.1e-177  576.4   6.3    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_3715  Ga0059261_3715 dihydrolipoamide 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3715  Ga0059261_3715 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  576.4   6.3  2.1e-177  2.1e-177       1     461 []       4     466 .]       4     466 .] 0.98

  Alignments for each domain:
  == domain 1  score: 576.4 bits;  conditional E-value: 2.1e-177
                                 TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgie 69 
                                               +ydv+v+G+GpgGYvaAira+qlglk+a+ve+e lGG+Cln+GCiPtKalL+sae+++ +++ak++g+ 
  lcl|FitnessBrowser__Korea:Ga0059261_3715   4 SYDVIVLGSGPGGYVAAIRASQLGLKTAIVERELLGGICLNWGCIPTKALLRSAEIFHFMQHAKDYGLA 72 
                                               59******************************************************************* PP

                                 TIGR01350  70 venvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniii 137
                                               +e+++ dle++++r++ v k+l++Gv++L+kknkv v++G++kl++k++++v++e+++ ++l+aknii+
  lcl|FitnessBrowser__Korea:Ga0059261_3715  73 AEKITADLEAVVKRSRGVAKQLNQGVTHLMKKNKVAVHFGTGKLTGKGKLSVTAEDGKvTELTAKNIIL 141
                                               *******************************************************99888999****** PP

                                 TIGR01350 138 AtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldril 206
                                               AtG++ r lp  l +d++ v+t+++a++ ke+p++l+++G+G+iG+Efas+++++G++vtv+e+ldri+
  lcl|FitnessBrowser__Korea:Ga0059261_3715 142 ATGARARDLPN-LPADGNKVWTYRHAMTPKEMPKKLLVIGSGAIGIEFASFYNDMGSEVTVVEMLDRIV 209
                                               ***********.99999**************************************************** PP

                                 TIGR01350 207 paldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk..evetleaekvLvavGrkpnlee 273
                                               p++da++s  l+k+lkk+g++i+t+akv ++ +++  v++++ +k  ++   +  +v+va+G  pn+ +
  lcl|FitnessBrowser__Korea:Ga0059261_3715 210 PVEDADISAHLEKALKKQGMTIMTGAKVDKIAADATGVKATITGKdgKAVDGQFSHVIVAIGIVPNTAD 278
                                               **************************************977766622455556689************* PP

                                 TIGR01350 274 lgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidykav 342
                                               +gl++lgv++d+rg++ +  +++tn++g+yaiGD+++++ LAh+As+egv+aae+iagk+++++d + +
  lcl|FitnessBrowser__Korea:Ga0059261_3715 279 IGLKELGVDVDDRGFLRTGPDCKTNIDGLYAIGDITAPPWLAHKASHEGVIAAEAIAGKHPHAMDPRNI 347
                                               ********************************************************************* PP

                                 TIGR01350 343 PsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivga 411
                                               P ++y++P++asvGlte++ake+g+evkvg+fpf  ngka+al+e +Gfvk+++d ktge+lGah++ga
  lcl|FitnessBrowser__Korea:Ga0059261_3715 348 PGCTYCHPQIASVGLTEAKAKEAGYEVKVGNFPFIGNGKAIALGEPEGFVKTVFDAKTGELLGAHMIGA 416
                                               ********************************************************************* PP

                                 TIGR01350 412 easeliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                               e++e+i+  ++  +le+t+ el++t++pHPt+sE+++ea+laa+g+++h+
  lcl|FitnessBrowser__Korea:Ga0059261_3715 417 EVTEMIQGYTIGKTLETTEAELMETVFPHPTISETMHEAVLAAYGRQLHM 466
                                               ***********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (466 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.81
//
[ok]

This GapMind analysis is from Sep 17 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