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 dihydrolipoamide dehydrogenase Dld1; EC 1.8.1.4 (characterized)
to candidate CA265_RS24150 CA265_RS24150 dihydrolipoyl dehydrogenase

Query= CharProtDB::CH_124461
         (511 letters)



>FitnessBrowser__Pedo557:CA265_RS24150
          Length = 468

 Score =  480 bits (1235), Expect = e-140
 Identities = 244/468 (52%), Positives = 329/468 (70%), Gaps = 4/468 (0%)

Query: 45  EYDLCVIGGGPGGYVAAIRGAQLGLKTICVEKRGTLGGTCLNVGCIPSKALLNNSHIYHT 104
           +YD+ VIG GPGGYV AIR AQLGLKT  VEK  T GGTCLNVGCIPSKALL++S  +H 
Sbjct: 2   QYDVVVIGSGPGGYVGAIRCAQLGLKTAVVEKYKTFGGTCLNVGCIPSKALLDSSEHFHN 61

Query: 105 VKHDTKRRGIDVSGVSVNLSQMMKAKDDSVKSLTSGIEYLFKKNKVEYAKGTGSFIDPQT 164
             H     GI++  + V++ QM+  KDD V   T+GI YLFKKNK++  +G GSF+D  T
Sbjct: 62  AAHTFTTHGINLKDLKVDMKQMIARKDDVVAQNTAGITYLFKKNKIDSFEGVGSFVDKNT 121

Query: 165 LSVKGIDGAADQTIKAKNFIIATGSEVKPFPGVTIDEKKIVSSTGALSLSEVPKKMTVLG 224
           + V   DG+ + T+ AKN IIATGS+    P + ID+K+I++ST AL++ EVPK M V+G
Sbjct: 122 ILVTKADGSTE-TLSAKNVIIATGSKPTALPFLPIDKKRIITSTEALNIKEVPKTMVVIG 180

Query: 225 GGIIGLEMGSVWSRLGAEVTVVEFLPAVGGPMDADISKALSRIISKQ-GIKFKTSTKLLS 283
           GG+IGLE+GSV++RLG +V+VVEFLP++ G MDA + K L R++ K  G++F    K+  
Sbjct: 181 GGVIGLELGSVYARLGTKVSVVEFLPSIIGTMDAGLGKELQRVLKKTLGMEFYMGHKVTG 240

Query: 284 AKVNGDSVEVEIENMKNNKRETYQTDVLLVAIGRVPYTEGLGLDKLGISMDKSNRVIMDS 343
           A   G +V V  +  K     + + D  +VA+GR  Y+EGLGLDK+GI++++  + I  +
Sbjct: 241 ATTKGKTVTVTADTPKGESI-SLEADYCIVAVGRTAYSEGLGLDKIGITVEERGKKIPVN 299

Query: 344 EY-RTNIPHIRVIGDATLGPMLAHKAEDEGIAAVEYIAKGQGHVNYNCIPAVMYTHPEVA 402
           E+  T++  +  IGD   G MLAHKAEDEG    E IA  + H+NYN IP V+YT PEVA
Sbjct: 300 EHLETSVKGVYAIGDVITGAMLAHKAEDEGTYVAETIAGQKPHINYNLIPGVVYTWPEVA 359

Query: 403 WVGITEQKAKESGIKYRIGTFPFSANSRAKTNMDADGLVKVIVDAETDRLLGVHMIGPMA 462
            VG+TE++ KE G+KY+ G+FPF A+ RAK +MD DG +KV+ DA TD +LGVHMIGP A
Sbjct: 360 SVGLTEEQLKEKGVKYKAGSFPFKASGRAKASMDTDGFIKVLADAATDEVLGVHMIGPRA 419

Query: 463 GELIGEATLALEYGASAEDVARVCHAHPTLSEATKEAMMAAWCGKSIH 510
            ++I EA +A+E+ ASAED+AR CHAHPT +EA KEA +AA   ++IH
Sbjct: 420 ADMIAEAVIAMEFRASAEDIARTCHAHPTYTEALKEAALAATDNRAIH 467


Lambda     K      H
   0.316    0.134    0.383 

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: 616
Number of extensions: 29
Number of successful extensions: 5
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: 511
Length of database: 468
Length adjustment: 34
Effective length of query: 477
Effective length of database: 434
Effective search space:   207018
Effective search space used:   207018
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate CA265_RS24150 CA265_RS24150 (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.21673.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.5e-176  573.6  12.3   1.7e-176  573.4  12.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS24150  CA265_RS24150 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS24150  CA265_RS24150 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  573.4  12.3  1.7e-176  1.7e-176       1     460 [.       2     467 ..       2     468 .] 0.96

  Alignments for each domain:
  == domain 1  score: 573.4 bits;  conditional E-value: 1.7e-176
                                  TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvek.eklGGtClnvGCiPtKalLksaevveelke.akel 66 
                                                +ydvvviG+GpgGYv Air+aqlglk+a+vek +++GGtClnvGCiP+KalL s+e ++++ + + ++
  lcl|FitnessBrowser__Pedo557:CA265_RS24150   2 QYDVVVIGSGPGGYVGAIRCAQLGLKTAVVEKyKTFGGTCLNVGCIPSKALLDSSEHFHNAAHtFTTH 69 
                                                69******************************9*********************************** PP

                                  TIGR01350  67 gievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleak 133
                                                gi+++++k+d++++ +rk+ vv + ++G+++L+kknk+++++G ++++dk+++ v+k +++ ++l+ak
  lcl|FitnessBrowser__Pedo557:CA265_RS24150  70 GINLKDLKVDMKQMIARKDDVVAQNTAGITYLFKKNKIDSFEGVGSFVDKNTILVTKADGStETLSAK 137
                                                ********************************************************9998779***** PP

                                  TIGR01350 134 niiiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtviel 201
                                                n+iiAtGs+p++lp+ l  d+k++its+eal++kevp+++v++GgGviG+E++s++a+lG+kv+v+e+
  lcl|FitnessBrowser__Pedo557:CA265_RS24150 138 NVIIATGSKPTALPF-LPIDKKRIITSTEALNIKEVPKTMVVIGGGVIGLELGSVYARLGTKVSVVEF 204
                                                ***************.9999999********************************************* PP

                                  TIGR01350 202 ldrilpaldaevskvlkkklkkk.gvkiltnakvtevekeedevvveakkk..evetleaekvLvavG 266
                                                l+ i+ ++da + k+l++ lkk+ g+++++++kvt  +++ ++v+v+a+    e  +lea++ +vavG
  lcl|FitnessBrowser__Pedo557:CA265_RS24150 205 LPSIIGTMDAGLGKELQRVLKKTlGMEFYMGHKVTGATTKGKTVTVTADTPkgESISLEADYCIVAVG 272
                                                ********************98747**********99999999985554432488899********** PP

                                  TIGR01350 267 rkpnleelgleklgvelderg.aikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagke 333
                                                r++  e+lgl+k+g++++erg +i+v+e+l+t+v+g+yaiGDvi ++mLAh+A++eg+++ae+iag++
  lcl|FitnessBrowser__Pedo557:CA265_RS24150 273 RTAYSEGLGLDKIGITVEERGkKIPVNEHLETSVKGVYAIGDVITGAMLAHKAEDEGTYVAETIAGQK 340
                                                *******************9746*******************************************99 PP

                                  TIGR01350 334 kseidykavPsviytePevasvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktg 401
                                                + +i+y+++P v+yt PevasvGlteeq+ke+g+++k+g+fpf+a+g+a a+ +tdGf+kv++d  t+
  lcl|FitnessBrowser__Pedo557:CA265_RS24150 341 P-HINYNLIPGVVYTWPEVASVGLTEEQLKEKGVKYKAGSFPFKASGRAKASMDTDGFIKVLADAATD 407
                                                8.9***************************************************************** PP

                                  TIGR01350 402 eilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalgk.aih 460
                                                e+lG+h++g++a+++i+e+++a+e+++++e++a+t+h+HPt++Ea+keaalaa+++ aih
  lcl|FitnessBrowser__Pedo557:CA265_RS24150 408 EVLGVHMIGPRAADMIAEAVIAMEFRASAEDIARTCHAHPTYTEALKEAALAATDNrAIH 467
                                                **************************************************9998651555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (468 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: 10.40
//
[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, or view the source code.

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