GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N2C3

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate AO356_11880 AO356_11880 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_11880
          Length = 466

 Score =  711 bits (1836), Expect = 0.0
 Identities = 346/465 (74%), Positives = 402/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M +YDV+++G GPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MSNYDVVILGGGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA+G EFA LGI VSP L+LAQMMKQKDESV  LT+G+EFLFRK+KV WIKGW  + G 
Sbjct: 61  EAATGTEFANLGIEVSPTLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V   DG   +L A+DIVIATGSEP PLPGV +DNQRILDSTGAL L+EVPRHLVVI
Sbjct: 121 GKVTVTGDDGSKTELTAKDIVIATGSEPMPLPGVTIDNQRILDSTGALSLSEVPRHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+EYL+RICPG+DGE  +TLQRAL +QG++F+L ++V  
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTG 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +   GV+L ++PAAGG  + L ADYVLVAIGRRPYT+GLGLE VGL++D+RGML NQ 
Sbjct: 241 ATTSASGVQLQIEPAAGGEAQILDADYVLVAIGRRPYTQGLGLENVGLSTDKRGMLANQH 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ APGVWVIGDVT+GPMLAHKAE+EA+ CIE+IAG AAE+N  +IPSVIYT+PE+ASV
Sbjct: 301 HRTEAPGVWVIGDVTAGPMLAHKAEDEAMACIEQIAGKAAEVNYALIPSVIYTRPELASV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  EEQL+A  R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D++LGVH++GP VSE
Sbjct: 361 GQTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSE 420

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAM+V G A Q
Sbjct: 421 MIGEYCVAMEFSASAEDIALTCHPHPTRSEALRQAAMNVEGMATQ 465


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: 793
Number of extensions: 27
Number of successful extensions: 1
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: 466
Length adjustment: 33
Effective length of query: 434
Effective length of database: 433
Effective search space:   187922
Effective search space used:   187922
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 AO356_11880 AO356_11880 (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.24242.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-167  543.5   1.1   2.1e-167  543.4   1.1    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880  AO356_11880 dihydrolipoamide deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880  AO356_11880 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  543.4   1.1  2.1e-167  2.1e-167       1     460 [.       3     465 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 543.4 bits;  conditional E-value: 2.1e-167
                                       TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke 62 
                                                     +ydvv++GgGpgGY aAira+qlglk a+ve   +lGGtClnvGC+P+KalL+++e++e ++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880   3 NYDVVILGGGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASELYEAATG 65 
                                                     69*****************************8799************************9875 PP

                                       TIGR01350  63 ..akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkk 123
                                                       +++lgiev + +l+l++++++k++ v+ l++G+++L++knkv+ ikG +++ ++++v+v++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880  66 teFANLGIEV-SPTLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGPGKVTVTG 127
                                                     5699****88.789************************************************9 PP

                                       TIGR01350 124 ekke.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEf 185
                                                     ++++ ++l+ak+i+iAtGsep  lp+ +  d++++++s++al+l+evp++lv++G+GviG+E+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 128 DDGSkTELTAKDIVIATGSEPMPLPG-VTIDNQRILDSTGALSLSEVPRHLVVIGAGVIGLEL 189
                                                     998867899*****************.9999999***************************** PP

                                       TIGR01350 186 asifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..v 246
                                                     +s++++lG++vtv+e+ldri+p +d e  k+l+++l k+g++++ ++kvt  ++++  v+  +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 190 GSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTGATTSASGVQlqI 252
                                                     **************************************************7777777777335 PP

                                       TIGR01350 247 eakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDv 308
                                                     e   + e++ l+a++vLva+Gr+p +++lgle++g+++d+rg +  +++ rt++pg+++iGDv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 253 EPAAGgEAQILDADYVLVAIGRRPYTQGLGLENVGLSTDKRG-MLANQHHRTEAPGVWVIGDV 314
                                                     5555569*********************************99.567***************** PP

                                       TIGR01350 309 igklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkv 371
                                                     ++++mLAh+A++e++ ++e+iagk++ e++y ++Psviyt+Pe+asvG teeq+k+eg ++kv
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 315 TAGPMLAHKAEDEAMACIEQIAGKAA-EVNYALIPSVIYTRPELASVGQTEEQLKAEGRAYKV 376
                                                     ***********************887.9*********************************** PP

                                       TIGR01350 372 gkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveela 434
                                                     gkfpf+an++a + +et+Gf+kv++d+ t+eilG+h+vg+++se+i e  +a+e+ +++e++a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 377 GKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSEMIGEYCVAMEFSASAEDIA 439
                                                     *************************************************************** PP

                                       TIGR01350 435 ktihpHPtlsEaikeaalaalgkaih 460
                                                      t+hpHPt sEa+ +aa ++ g+a +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_11880 440 LTCHPHPTRSEALRQAAMNVEGMATQ 465
                                                     ******************99988765 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.01
//
[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:

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:

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:

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:

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