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

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.30152.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.95
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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