Alignments for a candidate for lpd in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Synechococcus elongatus PCC 7942

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Synpcc7942_1198 Synpcc7942_1198 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0K9R8G5
         (565 letters)



>FitnessBrowser__SynE:Synpcc7942_1198
          Length = 479

 Score =  556 bits (1434), Expect = e-163
 Identities = 284/474 (59%), Positives = 358/474 (75%), Gaps = 9/474 (1%)

Query: 81  FDYDLLIIGAGVGGHGAALHAVEKGLKTAIIEGDVMGGTCVNRGCVPSKALLAVSGRMRE 140
           FDYD+++IGAG GG  AA HA EKGLKTAI+E   +GGTCVNRGCVPSKALLA SGR+RE
Sbjct: 5   FDYDVIVIGAGYGGFDAAKHACEKGLKTAIVEARDLGGTCVNRGCVPSKALLAASGRVRE 64

Query: 141 LQNEQHLKSFGIQVGAANYDRQGVADHASNLASKIRGNLTNSLKALGVDILTGFGTILGP 200
           + +  HL++FGIQV   ++DRQ +ADHA+NL   +R NL N+LK LG +IL G G + G 
Sbjct: 65  ITDTDHLQNFGIQVQGVSFDRQAIADHAANLVDTVRTNLGNTLKRLGAEILMGRGRLAGS 124

Query: 201 QKVQF----GKDNIVTAKDIIIATGSVPFVPRGIEVDGKTVITSDHALKLESVPDWIAIV 256
           Q+V      G +   +A+D+I+ATGS PFVP GIE+DGKTV TSD ALKLE++P WIAI+
Sbjct: 125 QRVTVTAADGTEKTYSARDVILATGSDPFVPPGIEIDGKTVFTSDDALKLETLPQWIAII 184

Query: 257 GSGYIGLEFSDVYTALGSEVTFIEALDQLMPGFDPEVSKLAQRILINPRKIDYHTGVFAT 316
           GSGYIGLEFSDVYTALG EVT IEALD+L+P FDP+V+K+AQR L++ R I+  TGV A 
Sbjct: 185 GSGYIGLEFSDVYTALGCEVTMIEALDRLLPTFDPDVAKVAQRSLLDGRDIETRTGVLAR 244

Query: 317 KITPAKDGKPVTIELTDAKTKEHKDTLEVDAALIATGRAPYTQGLGLESINV-VTQRGFV 375
           KITP   G PV IEL D +TKE  + LEVDA L+ATGR P T+ LGLE++ V V +RGF+
Sbjct: 245 KITP---GSPVVIELADFETKELVEVLEVDACLVATGRIPSTKNLGLETVAVEVDRRGFI 301

Query: 376 PVDDRMRVIDANGKLVPNLYCIGDANGKMMLAHAASAQGISVVEQVTGRDHVLNHLSIPA 435
           PVDD MRV+  + K VP+L+ +GDA GK+MLAHAA+AQG+  +E +TG    +++ SIPA
Sbjct: 302 PVDDGMRVL-RDSKPVPHLFAVGDATGKLMLAHAAAAQGVVAIENITGHPRSVDYRSIPA 360

Query: 436 ACFTHPEISMVGLTEPQAREKAEKEGFPVSVAKTSFKANSKALAENEAEGIAKLIYRPDN 495
           A FTHPEIS VGL+E  A+    +EGF V   ++ FKANSKALAE +A+G AK+++R D 
Sbjct: 361 ATFTHPEISSVGLSEADAKALGGQEGFEVGSVRSYFKANSKALAEADADGFAKVLFRKDT 420

Query: 496 GEILGVHIFGLHAADLIHEASNAIAMGTPIQDLKLAVHAHPTLSEVLDELYKAA 549
           GE+LG HIFGLHAADLI E +NAIA    +++L   VH HPTLSEV++  YK A
Sbjct: 421 GEVLGAHIFGLHAADLIQEVANAIARRQSVKELAFEVHTHPTLSEVIESAYKQA 474


Lambda     K      H
   0.316    0.133    0.377 

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: 709
Number of extensions: 28
Number of successful extensions: 6
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: 565
Length of database: 479
Length adjustment: 35
Effective length of query: 530
Effective length of database: 444
Effective search space:   235320
Effective search space used:   235320
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 Synpcc7942_1198 Synpcc7942_1198 (dihydrolipoamide 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.17123.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-135  435.8   0.1     1e-134  435.6   0.1    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1198  Synpcc7942_1198 dihydrolipoamide


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1198  Synpcc7942_1198 dihydrolipoamide dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  435.6   0.1    1e-134    1e-134       2     456 ..       7     476 ..       6     479 .] 0.92

  Alignments for each domain:
  == domain 1  score: 435.6 bits;  conditional E-value: 1e-134
                                 TIGR01350   2 ydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelke...akelg 67 
                                               ydv+viG+G gG+ aA +a ++glk+a+ve ++lGGtC+n+GC+P+KalL+++  v+e+++   ++++g
  lcl|FitnessBrowser__SynE:Synpcc7942_1198   7 YDVIVIGAGYGGFDAAKHACEKGLKTAIVEARDLGGTCVNRGCVPSKALLAASGRVREITDtdhLQNFG 75 
                                               9****************************************************99998864334899** PP

                                 TIGR01350  68 ievenvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakni 135
                                               i+v++v++d +++ ++  + v+++++ +   lk+ + e ++G+++l ++++v+v++ +++ k+++a ++
  lcl|FitnessBrowser__SynE:Synpcc7942_1198  76 IQVQGVSFDRQAIADHAANLVDTVRTNLGNTLKRLGAEILMGRGRLAGSQRVTVTAADGTeKTYSARDV 144
                                               *******************************************************999877999***** PP

                                 TIGR01350 136 iiAtGseprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldr 204
                                               i+AtGs+p  +p+ +e d+k+v ts++al+l+++p+ ++i+G+G+iG+Ef+ +++ lG++vt+ie+ldr
  lcl|FitnessBrowser__SynE:Synpcc7942_1198 145 ILATGSDPFVPPG-IEIDGKTVFTSDDALKLETLPQWIAIIGSGYIGLEFSDVYTALGCEVTMIEALDR 212
                                               *************.******************************************************* PP

                                 TIGR01350 205 ilpaldaevskvlkkklkk.kgvkiltnakvtevekeedevv..veakkk.evetleaekvLvavGrkp 269
                                               +lp++d +v+kv++++l + + ++  t+    +++  +  v   +  + k  ve+le+++ Lva Gr p
  lcl|FitnessBrowser__SynE:Synpcc7942_1198 213 LLPTFDPDVAKVAQRSLLDgRDIETRTGVLARKITPGSPVVIelADFETKeLVEVLEVDACLVATGRIP 281
                                               **************9986514466666666667777777666774444443589*************** PP

                                 TIGR01350 270 nleelgleklgveldergaikvdeelrt.....nvpgiyaiGDvigklmLAhvAskegvvaaekiagke 333
                                               ++++lgle++ ve+d+rg+i+vd+ +r+      vp+++a+GD++gklmLAh A ++gvva+e+i+g+ 
  lcl|FitnessBrowser__SynE:Synpcc7942_1198 282 STKNLGLETVAVEVDRRGFIPVDDGMRVlrdskPVPHLFAVGDATGKLMLAHAAAAQGVVAIENITGHP 350
                                               **************************98433334899******************************66 PP

                                 TIGR01350 334 kseidykavPsviytePevasvGlteeqak....eegievkvgkfpfaangkalaleetdGfvkvivdk 398
                                               + ++dy+ +P++++t+Pe++svGl+e++ak    +eg ev +++  f+an+kala  ++dGf+kv++ k
  lcl|FitnessBrowser__SynE:Synpcc7942_1198 351 R-SVDYRSIPAATFTHPEISSVGLSEADAKalggQEGFEVGSVRSYFKANSKALAEADADGFAKVLFRK 418
                                               6.9***************************33333568999999************************* PP

                                 TIGR01350 399 ktgeilGahivgaeaseliselalaveleltveelaktihpHPtlsEaikeaalaalg 456
                                               +tge+lGahi g +a++li+e+a a++ +++v+ela  +h+HPtlsE+i+ a ++a +
  lcl|FitnessBrowser__SynE:Synpcc7942_1198 419 DTGEVLGAHIFGLHAADLIQEVANAIARRQSVKELAFEVHTHPTLSEVIESAYKQAAT 476
                                               ****************************************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (479 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: 9.55
//
[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