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.4755.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.79
//
[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