Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pseudomonas fluorescens GW456-L13

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate PfGW456L13_698 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698
          Length = 466

 Score =  698 bits (1801), Expect = 0.0
 Identities = 337/465 (72%), Positives = 399/465 (85%)

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

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA G EFA LGI V P L+L QMMKQKDESV  LT+G+EFLFRK+KV WI+GW  + G 
Sbjct: 61  DAAKGAEFANLGIEVKPVLNLNQMMKQKDESVTGLTKGIEFLFRKNKVDWIRGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V  + GG  +L ARDI+IATGSEP PLPGV +DN+RILDSTGAL L EVP+HLVVI
Sbjct: 121 GKVTVTDSAGGKTELSARDIIIATGSEPTPLPGVDIDNKRILDSTGALALTEVPKHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+E+L+RICPG+D E  +TLQR+L++QG+ F+L ++V +
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDIEAGKTLQRSLSKQGLSFKLSSKVTS 240

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

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ A GVWVIGDVTSGPMLAHKAE+EA+ C+E++ G A E+N  +IPSV+YT+PE+ASV
Sbjct: 301 HRTEAVGVWVIGDVTSGPMLAHKAEDEAMACVEQMVGKAGEVNYNLIPSVVYTKPELASV 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+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: 776
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 PfGW456L13_698 (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.8874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   5.2e-164  532.2   1.2   5.8e-164  532.1   1.2    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698  Dihydrolipoamide dehydrogenase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698  Dihydrolipoamide dehydrogenase (EC 1.8.1.4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.1   1.2  5.8e-164  5.8e-164       2     460 ..       4     465 ..       3     466 .] 0.96

  Alignments for each domain:
  == domain 1  score: 532.1 bits;  conditional E-value: 5.8e-164
                                              TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaev 56 
                                                            ydvv++GgGpgGY aAira+qlglk a+ve   +lGGtClnvGC+P+KalL+++e+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698   4 YDVVILGGGPGGYNAAIRAGQLGLKAACVEGrATLGGTCLNVGCMPSKALLHASEL 59 
                                                            9*****************************8799********************** PP

                                              TIGR01350  57 veelke..akelgievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGe 110
                                                            ++ +k   +++lgiev+   l+l++++++k++ v+ l++G+++L++knkv+ i G 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698  60 YDAAKGaeFANLGIEVK-PVLNLNQMMKQKDESVTGLTKGIEFLFRKNKVDWIRGW 114
                                                            ***99756899999985.679*********************************** PP

                                              TIGR01350 111 aklldkkevevkkekke.kkleakniiiAtGseprelplkleedekvvitseeale 165
                                                            +++ ++++v+v+++++  ++l+a +iiiAtGsep+ lp+ ++ d+k++++s++al+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 115 GHIDGPGKVTVTDSAGGkTELSARDIIIATGSEPTPLPG-VDIDNKRILDSTGALA 169
                                                            *************997757899*****************.**************** PP

                                              TIGR01350 166 lkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkkl 221
                                                            l+evp++lv++G+GviG+E++s++++lG++vtv+e+ldri+p +d e  k+l+++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 170 LTEVPKHLVVIGAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDIEAGKTLQRSL 225
                                                            ******************************************************** PP

                                              TIGR01350 222 kkkgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkpnleel 274
                                                            +k+g++++ ++kvt+ ++++  v+  +e   +  +e lea++vLva+Gr+p +++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 226 SKQGLSFKLSSKVTSATTSATGVQlsIEPAAGgAAELLEADYVLVAIGRRPYTQGL 281
                                                            **************888888888844555555589********************* PP

                                              TIGR01350 275 gleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekia 330
                                                            gle++g+ +d+rg+   ++  rt++ g+++iGDv++++mLAh+A++e++ ++e+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 282 GLENVGLATDKRGM-LANKGHRTEAVGVWVIGDVTSGPMLAHKAEDEAMACVEQMV 336
                                                            ***********995.57999************************************ PP

                                              TIGR01350 331 gkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalale 386
                                                            gk+  e++y+++Psv+yt+Pe+asvG+teeq+k+eg ++kvgkfpf+an++a + +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 337 GKAG-EVNYNLIPSVVYTKPELASVGKTEEQLKAEGRAYKVGKFPFTANSRAKINH 391
                                                            *998.9************************************************** PP

                                              TIGR01350 387 etdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPt 442
                                                            et+Gf+kv++d+ t+e+lG+h+vg+++se+i e  +a+e+ +++e++a t+hpHPt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 392 ETEGFAKVLADERTDEVLGVHLVGPSVSEMIGEYCVAMEFSASAEDIALTCHPHPT 447
                                                            ******************************************************** PP

                                              TIGR01350 443 lsEaikeaalaalgkaih 460
                                                             sEa+ +aa ++ g+a +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_698 448 RSEALRQAAMNVEGMATQ 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: 7.81
//
[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