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_1343 Ga0059261_1343 dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__Korea:Ga0059261_1343
          Length = 464

 Score =  513 bits (1321), Expect = e-150
 Identities = 261/463 (56%), Positives = 345/463 (74%), Gaps = 12/463 (2%)

Query: 5   YDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELYAAA 64
           +DV+VIG+GPGGY AAIRA QLGLK AC EGRETLGGTCLNVGC+PSKALLHASELY  A
Sbjct: 6   FDVLVIGSGPGGYVAAIRAAQLGLKTACAEGRETLGGTCLNVGCIPSKALLHASELYEEA 65

Query: 65  SGGEFARLGIRVSP-ELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGEGR 123
           + G  A+LG+++   ELDL  M  Q+ ++V  LT G+EFLF+K+KV+W+KG+A   G+  
Sbjct: 66  ASGALAKLGVKLGKVELDLDAMHAQRLDAVKGLTGGIEFLFKKNKVEWLKGYATFTGKDS 125

Query: 124 VGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVIGA 183
           V V     G  ++ A++IVIATGS   PLPGV +D + ++DSTGALELA+VP HLVVIG 
Sbjct: 126 VKV-----GDREVRAKNIVIATGSSVTPLPGVEIDQKIVVDSTGALELAKVPEHLVVIGG 180

Query: 184 GVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRV--VA 241
           GVIGLELGSVWRR+GA+VTV+EYL++I PG D +  +   R   +QG+ F+ GT+V  VA
Sbjct: 181 GVIGLELGSVWRRVGAKVTVVEYLDQILPGFDADVRKEAARLFKKQGIEFKTGTKVTGVA 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLE-NQ 300
            + G+    + ++PAAGGA E+++AD VLVAIGR+P T+GLGL+  GL  ++RG +E + 
Sbjct: 241 VKGGK--ATITVEPAAGGAAETIEADNVLVAIGRKPNTDGLGLDAAGLTVNQRGQIETDH 298

Query: 301 GQRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVAS 360
             +++ PG+W IGDV  GPMLAHKAE+E I   E IAG    +N +VIPSV+YT PE+A 
Sbjct: 299 SFKTSVPGIWAIGDVIPGPMLAHKAEDEGIAVAENIAGLTGIVNHDVIPSVVYTMPEIAG 358

Query: 361 VGLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVS 420
           VGL EE  + A+ E KVG+FP + NSRAK NHE +GF+K+++DA++D+VLGV +I     
Sbjct: 359 VGLTEEAAK-AKGEVKVGKFPMAGNSRAKTNHEPDGFVKVIADAKTDRVLGVWIITSVAG 417

Query: 421 EMIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGR 463
            MI +A  AMEF A++ED+A TCH HPT SEA+++AAM V G+
Sbjct: 418 TMIAQAAQAMEFGATSEDIAYTCHAHPTHSEAIKEAAMAVTGK 460


Lambda     K      H
   0.318    0.135    0.390 

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: 689
Number of extensions: 29
Number of successful extensions: 5
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: 467
Length of database: 464
Length adjustment: 33
Effective length of query: 434
Effective length of database: 431
Effective search space:   187054
Effective search space used:   187054
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Ga0059261_1343 Ga0059261_1343 (dihydrolipoamide dehydrogenase (EC 1.8.1.4))
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.22859.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-168  546.2  12.0   3.5e-168  546.0  12.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_1343  Ga0059261_1343 dihydrolipoamide 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_1343  Ga0059261_1343 dihydrolipoamide dehydrogenase (EC 1.8.1.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  546.0  12.0  3.5e-168  3.5e-168       2     461 .]       6     464 .]       5     464 .] 0.97

  Alignments for each domain:
  == domain 1  score: 546.0 bits;  conditional E-value: 3.5e-168
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke..akelg 67 
                                               +dv+viG+GpgGYvaAiraaqlglk+a+ e  e+lGGtClnvGCiP+KalL+++e++ee+    +++lg
  lcl|FitnessBrowser__Korea:Ga0059261_1343   6 FDVLVIGSGPGGYVAAIRAAQLGLKTACAEGrETLGGTCLNVGCIPSKALLHASELYEEAASgaLAKLG 74 
                                               8*****************************879**************************9988899*** PP

                                 TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleaknii 136
                                               +++ +v+ldl+++++++   vk l+gG+++L+kknkve +kG+a++++k++v+v +++    ++akni+
  lcl|FitnessBrowser__Korea:Ga0059261_1343  75 VKLGKVELDLDAMHAQRLDAVKGLTGGIEFLFKKNKVEWLKGYATFTGKDSVKVGDRE----VRAKNIV 139
                                               ******************************************************9998....78***** PP

                                 TIGR01350 137 iAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldri 205
                                               iAtGs+++ lp+ +e d+k+v++s++alel +vpe+lv++GgGviG+E++s+++++G+kvtv+e+ld+i
  lcl|FitnessBrowser__Korea:Ga0059261_1343 140 IATGSSVTPLPG-VEIDQKIVVDSTGALELAKVPEHLVVIGGGVIGLELGSVWRRVGAKVTVVEYLDQI 207
                                               ************.******************************************************** PP

                                 TIGR01350 206 lpaldaevskvlkkklkkkgvkiltnakvt..evekeedevvveakkk.evetleaekvLvavGrkpnl 271
                                               lp +da+v k++++ +kk+g++++t++kvt  +v+  +++++ve   +  +et+ea++vLva+Grkpn+
  lcl|FitnessBrowser__Korea:Ga0059261_1343 208 LPGFDADVRKEAARLFKKQGIEFKTGTKVTgvAVKGGKATITVEPAAGgAAETIEADNVLVAIGRKPNT 276
                                               ******************************666777777777887776699****************** PP

                                 TIGR01350 272 eelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseidyk 340
                                               ++lgl++ g+++++rg+i++d++++t+vpgi+aiGDvi ++mLAh+A++eg+ +ae+iag +   ++++
  lcl|FitnessBrowser__Korea:Ga0059261_1343 277 DGLGLDAAGLTVNQRGQIETDHSFKTSVPGIWAIGDVIPGPMLAHKAEDEGIAVAENIAGLTG-IVNHD 344
                                               ************************************************************887.9**** PP

                                 TIGR01350 341 avPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahiv 409
                                               ++Psv+yt Pe+a vGltee ak++  evkvgkfp+a n++a + +e dGfvkvi+d kt+++lG+ i+
  lcl|FitnessBrowser__Korea:Ga0059261_1343 345 VIPSVVYTMPEIAGVGLTEEAAKAK-GEVKVGKFPMAGNSRAKTNHEPDGFVKVIADAKTDRVLGVWII 412
                                               ***********************99.79***************************************** PP

                                 TIGR01350 410 gaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaihv 461
                                                  a  +i+++a a+e+++t+e++a t+h+HPt sEaikeaa a++gk+ih+
  lcl|FitnessBrowser__Korea:Ga0059261_1343 413 TSVAGTMIAQAAQAMEFGATSEDIAYTCHAHPTHSEAIKEAAMAVTGKPIHI 464
                                               **************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (464 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: 7.24
//
[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