GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Phaeobacter inhibens BS107

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate GFF1715 PGA1_c17390 dihydrolipoyl dehydrogenase LpdA

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Phaeo:GFF1715
          Length = 464

 Score =  541 bits (1393), Expect = e-158
 Identities = 268/464 (57%), Positives = 350/464 (75%), Gaps = 3/464 (0%)

Query: 2   ADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYH 61
           A+ +D+IV+G GPGGYVAAIRAAQL LK  +VER H+GGICLNWGCIPTK+LLRS+EV+H
Sbjct: 3   AETYDVIVIGAGPGGYVAAIRAAQLGLKTCIVEREHMGGICLNWGCIPTKALLRSSEVFH 62

Query: 62  EMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQ 121
            M+ A+ +GL +    +DLD ++ RSR VA +L+SG+  L++KNK+ V+ G   L    +
Sbjct: 63  LMERAKDFGLKADNIGYDLDAVVKRSRGVAKQLSSGIGHLMKKNKIAVVMGEATLPAKGK 122

Query: 122 MLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGS 181
           + V+T +G ++ L AK+I++ATGARAR+LP + +DG  +WTY HAL P  MPKKLLVIGS
Sbjct: 123 VSVKTEKGTQE-LAAKNIVLATGARARELPGLEADGDLVWTYKHALDPVRMPKKLLVIGS 181

Query: 182 GAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLT 241
           GAIGIEFASFY   GA+ ++VE   ++LP+EDAE+SA+  KAF K+G++I+ ++ ++ L 
Sbjct: 182 GAIGIEFASFYNTLGADTTVVEVMDRVLPVEDAEISAFAKKAFVKQGMKIMEKAMVKQLD 241

Query: 242 PDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRT 301
                VTA I    GKV K+ F   I A+G+V NVE +GLD LG+K+DR  +  D + RT
Sbjct: 242 RGKGKVTAHIE-VGGKVEKQEFDTVISAVGIVGNVEGLGLDGLGVKVDRTHVVTDEYCRT 300

Query: 302 NVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVG 361
            VD ++AIGD+AGAP LAHKASH+GV+ AE IAG  H H +  ++I GCTY +PQVASVG
Sbjct: 301 GVDGLYAIGDIAGAPWLAHKASHEGVMVAELIAG-KHAHAVKPESIAGCTYCQPQVASVG 359

Query: 362 LTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEM 421
            TE KA++ GY++K+G FPFI NGKAIA G  +G VKT+FDA +G LLGAHMVGAEVTEM
Sbjct: 360 YTEAKAKELGYDIKVGRFPFIGNGKAIALGEAEGMVKTIFDAKTGELLGAHMVGAEVTEM 419

Query: 422 IQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           IQGY V R LETTE ++M T+FPHPTLSE MHESVL A+ R +H
Sbjct: 420 IQGYVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAFDRVIH 463


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: 671
Number of extensions: 35
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: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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 GFF1715 PGA1_c17390 (dihydrolipoyl dehydrogenase LpdA)
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.1071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     9e-174  564.4  10.8     1e-173  564.2  10.8    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1715  PGA1_c17390 dihydrolipoyl dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1715  PGA1_c17390 dihydrolipoyl dehydrogenase LpdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  564.2  10.8    1e-173    1e-173       2     461 .]       6     464 .]       5     464 .] 0.99

  Alignments for each domain:
  == domain 1  score: 564.2 bits;  conditional E-value: 1e-173
                          TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgievenvkldl 77 
                                        ydv+viG+GpgGYvaAiraaqlglk+ +ve+e++GG+Cln+GCiPtKalL+s+ev++ ++ ak++g++++n+ +dl
  lcl|FitnessBrowser__Phaeo:GFF1715   6 YDVIVIGAGPGGYVAAIRAAQLGLKTCIVEREHMGGICLNWGCIPTKALLRSSEVFHLMERAKDFGLKADNIGYDL 81 
                                        9*************************************************************************** PP

                          TIGR01350  78 ekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekkekkleakniiiAtGseprelplkleed 153
                                        +++++r++ v k+l++G+ +L+kknk+ v++Gea+l  k++v+vk+ek++++l akni++AtG++ relp+ le+d
  lcl|FitnessBrowser__Phaeo:GFF1715  82 DAVVKRSRGVAKQLSSGIGHLMKKNKIAVVMGEATLPAKGKVSVKTEKGTQELAAKNIVLATGARARELPG-LEAD 156
                                        ***********************************************************************.**** PP

                          TIGR01350 154 ekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldaevskvlkkklkkkgvkil 229
                                        +++v+t+++al   ++p++l+++G+G+iG+Efas++++lG++ tv+e++dr+lp++dae+s ++kk++ k+g+ki+
  lcl|FitnessBrowser__Phaeo:GFF1715 157 GDLVWTYKHALDPVRMPKKLLVIGSGAIGIEFASFYNTLGADTTVVEVMDRVLPVEDAEISAFAKKAFVKQGMKIM 232
                                        **************************************************************************** PP

                          TIGR01350 230 tnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgveldergaikvdeelrtnvpgiya 304
                                        ++a+v+++ + + +v+++++ + +ve+ e + v+ avG   n+e+lgl+ lgv++d+   +++de++rt v+g+ya
  lcl|FitnessBrowser__Phaeo:GFF1715 233 EKAMVKQLDRGKGKVTAHIEVGgKVEKQEFDTVISAVGIVGNVEGLGLDGLGVKVDR-THVVTDEYCRTGVDGLYA 307
                                        ****************77766668******************************999.77**************** PP

                          TIGR01350 305 iGDvigklmLAhvAskegvvaaekiagkekseidykavPsviytePevasvGlteeqakeegievkvgkfpfaang 380
                                        iGD++g + LAh+As+egv++ae iagk++++++ + +  ++y++P+vasvG+te++ake g+++kvg+fpf  ng
  lcl|FitnessBrowser__Phaeo:GFF1715 308 IGDIAGAPWLAHKASHEGVMVAELIAGKHAHAVKPESIAGCTYCQPQVASVGYTEAKAKELGYDIKVGRFPFIGNG 383
                                        **************************************************************************** PP

                          TIGR01350 381 kalaleetdGfvkvivdkktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                        ka+al+e++G+vk+i+d ktge+lGah+vgae++e+i+  ++  +le+t+e+l++t++pHPtlsE+++e++l+a++
  lcl|FitnessBrowser__Phaeo:GFF1715 384 KAIALGEAEGMVKTIFDAKTGELLGAHMVGAEVTEMIQGYVVGRQLETTEEDLMNTVFPHPTLSEMMHESVLDAFD 459
                                        **************************************************************************** PP

                          TIGR01350 457 kaihv 461
                                        + ih+
  lcl|FitnessBrowser__Phaeo:GFF1715 460 RVIHM 464
                                        ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (464 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.16
//
[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