Alignments for a candidate for lpd in Phaeobacter inhibens BS107

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.19601.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.68
//
[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