Alignments for a candidate for lpd in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Pedobacter sp. GW460-11-11-14-LB5

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate CA265_RS05155 CA265_RS05155 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Pedo557:CA265_RS05155
          Length = 462

 Score =  462 bits (1189), Expect = e-134
 Identities = 234/462 (50%), Positives = 321/462 (69%), Gaps = 2/462 (0%)

Query: 4   HFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEM 63
           ++D+IVLG GPGGYVAAIRA+QL LKVA+VER  LGGICLNWGCIPTK+LL+SA+V+  +
Sbjct: 2   NYDVIVLGSGPGGYVAAIRASQLGLKVAIVERESLGGICLNWGCIPTKALLKSAQVFEYI 61

Query: 64  QNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQML 123
            +A  YG+T+     D   ++ RSR VA  ++ GV+ L++KNK++VI G G++    ++ 
Sbjct: 62  NHAADYGITTAGATADFAAVVKRSRGVADGMSKGVQFLMKKNKIDVIMGTGKVKPGNKLE 121

Query: 124 VETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGA 183
           V+  +G ++ L AK+IIIATGAR+R+LPN+  DGK I  Y  A+  P +PK ++V+GSGA
Sbjct: 122 VKGADGSQQELSAKNIIIATGARSRELPNLKQDGKKIIGYRQAMVLPELPKSMVVVGSGA 181

Query: 184 IGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPD 243
           IG+EFA FYA  G +V+IVE    ++P+ED +VS  + ++ KK GI ++T ++++++   
Sbjct: 182 IGVEFAYFYATMGTKVTIVEFMDNVVPVEDEDVSKQLLRSLKKVGIDVMTSASVESVDTS 241

Query: 244 DEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNV 303
             G    +  A G  T E     + A G+VAN+ENIGL++ GIK ++G I  D F  T+V
Sbjct: 242 GAGCKVSVKTASGMQTIEA-DIVLSAAGIVANIENIGLEETGIKTEKGKIVTDEFYNTSV 300

Query: 304 DHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLT 363
              +AIGDV G   LAH AS +G+I  E IAG  H  PL+  NIPGCTY  P++ASVG T
Sbjct: 301 KGYYAIGDVVGGQALAHVASAEGIICVEKIAG-QHAEPLDYNNIPGCTYCTPEIASVGYT 359

Query: 364 EEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQ 423
           E+ A+  GY +KIG FPF A+GKA A GA DGFVK +FDA  G LLGAHM+GA VTEMI 
Sbjct: 360 EKAAKAAGYELKIGKFPFSASGKASAAGAKDGFVKLIFDAKYGELLGAHMIGANVTEMIA 419

Query: 424 GYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
              VAR LETT  E+++++ PHPT+SEA+ E+   AYG  +H
Sbjct: 420 EIVVARKLETTGHEMIKSVHPHPTMSEAIMEAAADAYGEVIH 461


Lambda     K      H
   0.319    0.135    0.393 

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: 601
Number of extensions: 21
Number of successful extensions: 4
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: 466
Length of database: 462
Length adjustment: 33
Effective length of query: 433
Effective length of database: 429
Effective search space:   185757
Effective search space used:   185757
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS05155 CA265_RS05155 (dihydrolipoyl 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.23878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   2.7e-176  572.7  17.7     3e-176  572.6  17.7    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS05155  CA265_RS05155 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS05155  CA265_RS05155 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  572.6  17.7    3e-176    3e-176       1     460 [.       2     461 ..       2     462 .] 0.99

  Alignments for each domain:
  == domain 1  score: 572.6 bits;  conditional E-value: 3e-176
                                  TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgi 68 
                                                +ydv+v+G+GpgGYvaAira+qlglkva+ve+e+lGG+Cln+GCiPtKalLksa+v+e++++a+++gi
  lcl|FitnessBrowser__Pedo557:CA265_RS05155   2 NYDVIVLGSGPGGYVAAIRASQLGLKVAIVERESLGGICLNWGCIPTKALLKSAQVFEYINHAADYGI 69 
                                                69****************************************************************** PP

                                  TIGR01350  69 evenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakni 135
                                                ++++ + d++++++r++ v + +++Gv++L+kknk++vi+G++k++  +++evk+ +++ ++l+akni
  lcl|FitnessBrowser__Pedo557:CA265_RS05155  70 TTAGATADFAAVVKRSRGVADGMSKGVQFLMKKNKIDVIMGTGKVKPGNKLEVKGADGSqQELSAKNI 137
                                                ******************************************************99987799****** PP

                                  TIGR01350 136 iiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielld 203
                                                iiAtG++ relp  l++d+k +i +++a+ l+e+p+s+v+vG+G+iGvEfa+++a++G+kvt++e++d
  lcl|FitnessBrowser__Pedo557:CA265_RS05155 138 IIATGARSRELPN-LKQDGKKIIGYRQAMVLPELPKSMVVVGSGAIGVEFAYFYATMGTKVTIVEFMD 204
                                                *************.****************************************************** PP

                                  TIGR01350 204 rilpaldaevskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpn 270
                                                +++p++d++vsk+l ++lkk g++++t+a+v++v ++ +  +v+ k    ++t+ea+ vL a G  +n
  lcl|FitnessBrowser__Pedo557:CA265_RS05155 205 NVVPVEDEDVSKQLLRSLKKVGIDVMTSASVESVDTSGAGCKVSVKTAsGMQTIEADIVLSAAGIVAN 272
                                                ************************************999999888877789***************** PP

                                  TIGR01350 271 leelgleklgveldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkekseid 338
                                                +e++gle++g+++++ g+i++de ++t+v+g yaiGDv+g+  LAhvAs+eg++++ekiag++++ +d
  lcl|FitnessBrowser__Pedo557:CA265_RS05155 273 IENIGLEETGIKTEK-GKIVTDEFYNTSVKGYYAIGDVVGGQALAHVASAEGIICVEKIAGQHAEPLD 339
                                                ************887.99************************************************** PP

                                  TIGR01350 339 ykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGa 406
                                                y+ +P ++y++Pe+asvG+te+ ak++g+e+k+gkfpf+a+gka a++ +dGfvk+i+d k+ge+lGa
  lcl|FitnessBrowser__Pedo557:CA265_RS05155 340 YNNIPGCTYCTPEIASVGYTEKAAKAAGYELKIGKFPFSASGKASAAGAKDGFVKLIFDAKYGELLGA 407
                                                ******************************************************************** PP

                                  TIGR01350 407 hivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                                h++ga+++e+i+e+++a +le+t +e+ k++hpHPt+sEai+eaa++a+g+ ih
  lcl|FitnessBrowser__Pedo557:CA265_RS05155 408 HMIGANVTEMIAEIVVARKLETTGHEMIKSVHPHPTMSEAIMEAAADAYGEVIH 461
                                                ***************************************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (462 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: 7.47
//
[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