GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf1N1B4_1976 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976
          Length = 466

 Score =  712 bits (1838), Expect = 0.0
 Identities = 346/465 (74%), Positives = 403/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M +YDV+++GAGPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MSTYDVVILGAGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA G EFA LGI V P L+LAQMMKQKDESV  LT+G+EFLFRK+KV WIKGW  + G 
Sbjct: 61  DAAMGAEFANLGIEVKPVLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G V V  + GG  QL A+DIVIATGSEP PLPGV +DN+RILDSTGAL L+EVP+HLVVI
Sbjct: 121 GSVTVTDSQGGKTQLTAKDIVIATGSEPTPLPGVDIDNKRILDSTGALSLSEVPKHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+E+L+RICPG+DGE  +TLQR+L++QG+RF+L ++V +
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDGEAGKTLQRSLSKQGIRFKLSSKVTS 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +   GV+L ++PAAGG  E L+ADYVLVAIGRRPYT+GLGLE VGLA+D+RGML N+G
Sbjct: 241 ATTSASGVQLSVEPAAGGTAELLEADYVLVAIGRRPYTQGLGLENVGLATDKRGMLANKG 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ A GVWVIGDVTSGPMLAHKAE+EA+ CIE+I G A E+N ++IPSVIYT+PE+ASV
Sbjct: 301 HRTEAAGVWVIGDVTSGPMLAHKAEDEAMACIEQIVGKAGEVNYDLIPSVIYTKPELASV 360

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

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAMDV G A Q
Sbjct: 421 MIGEYCVAMEFSASAEDIALTCHPHPTRSEALRQAAMDVEGMATQ 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: 800
Number of extensions: 26
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 Pf1N1B4_1976 (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.1203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.4e-166  538.8   1.2     6e-166  538.6   1.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976  Dihydrolipoamide dehydrogenase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976  Dihydrolipoamide dehydrogenase (EC 1.8.1.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.6   1.2    6e-166    6e-166       2     460 ..       4     465 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 538.6 bits;  conditional E-value: 6e-166
                                      TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.. 62 
                                                    ydvv++G+GpgGY aAira+qlglk a+ve   +lGGtClnvGC+P+KalL+++e+++ +    
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976   4 YDVVILGAGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASELYDAAMGae 67 
                                                    9*****************************8799************************986545 PP

                                      TIGR01350  63 akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekk 126
                                                    +++lgiev+   l+l++++++k++ v+ l++G+++L++knkv+ ikG +++ ++++v+v+++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976  68 FANLGIEVK-PVLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGPGSVTVTDSQG 130
                                                    899***985.679***********************************************9997 PP

                                      TIGR01350 127 e.kkleakniiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasif 189
                                                      ++l+ak+i+iAtGsep+ lp+ ++ d+k++++s++al+l+evp++lv++G+GviG+E++s++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 131 GkTQLTAKDIVIATGSEPTPLPG-VDIDNKRILDSTGALSLSEVPKHLVVIGAGVIGLELGSVW 193
                                                    76889******************.**************************************** PP

                                      TIGR01350 190 aklGvkvtvielldrilpaldaevskvlkkklkkkgvkiltnakvtevekeedevv..veakkk 251
                                                    ++lG++vtv+e+ldri+p +d e  k+l+++l+k+g++++ ++kvt+ ++++  v+  ve   +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 194 RRLGAQVTVVEFLDRICPGVDGEAGKTLQRSLSKQGIRFKLSSKVTSATTSASGVQlsVEPAAG 257
                                                    **********************************************888888888755665555 PP

                                      TIGR01350 252 .evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmL 314
                                                     ++e lea++vLva+Gr+p +++lgle++g+ +d+rg+   ++  rt+++g+++iGDv++++mL
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 258 gTAELLEADYVLVAIGRRPYTQGLGLENVGLATDKRGM-LANKGHRTEAAGVWVIGDVTSGPML 320
                                                    589********************************995.57999******************** PP

                                      TIGR01350 315 AhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaa 378
                                                    Ah+A++e++ ++e+i+gk+  e++y+++Psviyt+Pe+asvG+teeq+k+eg ++kvgkfpf+a
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 321 AHKAEDEAMACIEQIVGKAG-EVNYDLIPSVIYTKPELASVGKTEEQLKAEGRAYKVGKFPFTA 383
                                                    *****************998.9****************************************** PP

                                      TIGR01350 379 ngkalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPt 442
                                                    n++a + +et+Gf+kv++d+ t+e+lG+h+vg+++se+i e  +a+e+ +++e++a t+hpHPt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 384 NSRAKINHETEGFAKVLADERTDEVLGVHLVGPSVSEMIGEYCVAMEFSASAEDIALTCHPHPT 447
                                                    **************************************************************** PP

                                      TIGR01350 443 lsEaikeaalaalgkaih 460
                                                     sEa+ +aa ++ g+a +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976 448 RSEALRQAAMDVEGMATQ 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.66
//
[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