Alignments for a candidate for lpd in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for lpd in Klebsiella michiganensis M5al

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BWI76_RS14145 BWI76_RS14145 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Koxy:BWI76_RS14145
          Length = 465

 Score =  520 bits (1338), Expect = e-152
 Identities = 259/465 (55%), Positives = 334/465 (71%), Gaps = 1/465 (0%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           M D +D++++GGGPGGYVAAIRA QL L+ ALVE+ HLGGICLNWGCIPTK+LL  AEV 
Sbjct: 1   MHDKYDVLIIGGGPGGYVAAIRAGQLGLRTALVEKQHLGGICLNWGCIPTKALLHGAEVA 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
           H + +A+  G +  +  FDL K++  SR V+ +L  GV+ LL+KN V VI+G  +L G  
Sbjct: 61  HTIAHADRLGFSLSEVSFDLQKLVQFSRAVSQQLTGGVEYLLKKNGVTVIAGTARLRGKG 120

Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180
           Q+ V   +GEE+   A  +I+ATGAR R LP V  DG+ IWTY  AL+P  +P+ LL+IG
Sbjct: 121 QVTVADPQGEERDYRADHVILATGARPRALPGVEPDGERIWTYFEALQPERLPESLLIIG 180

Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240
           SGAIG+EFAS Y D G+ V++VE A QILP+EDAEVSA V K+F++RGI + +Q+ L  +
Sbjct: 181 SGAIGVEFASLYNDLGSNVTLVEQAAQILPVEDAEVSATVRKSFERRGIHVHSQTLLTQV 240

Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGR 300
              D GV   +     + T E     ++A GV  NVE +GL+ LG++LDRGFI  D   R
Sbjct: 241 KRTDTGVRCALKTTGAEQTLE-VERVLLAAGVQPNVEGLGLEALGVELDRGFIKTDAACR 299

Query: 301 TNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASV 360
           TNV  ++AIGDVAG PCLAHKASH+GVI  E +AG + V PLN   +PGCTYARPQVAS+
Sbjct: 300 TNVFGLYAIGDVAGPPCLAHKASHEGVICVETLAGVEGVRPLNCDYVPGCTYARPQVASL 359

Query: 361 GLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTE 420
           GLTE KAR+ G  +K+G F +  NGKA+A G T+GFVKT+FDA++G LLGAHMVG +VTE
Sbjct: 360 GLTEAKARETGRPIKVGKFAYQGNGKALASGETEGFVKTIFDAETGELLGAHMVGEQVTE 419

Query: 421 MIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
            IQG+ +A  LE T+  ++  IF HPTLSEAMHES+LAA G+ LH
Sbjct: 420 QIQGFGIAHHLEATDESLLSMIFAHPTLSEAMHESILAASGQPLH 464


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: 643
Number of extensions: 24
Number of successful extensions: 2
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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 BWI76_RS14145 BWI76_RS14145 (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.25358.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-172  560.6   0.0   1.5e-172  560.4   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS14145  BWI76_RS14145 dihydrolipoyl dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS14145  BWI76_RS14145 dihydrolipoyl dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.4   0.0  1.5e-172  1.5e-172       1     460 [.       4     464 ..       4     465 .] 0.98

  Alignments for each domain:
  == domain 1  score: 560.4 bits;  conditional E-value: 1.5e-172
                               TIGR01350   1 eydvvviGgGpgGYvaAiraaqlglkvalvekeklGGtClnvGCiPtKalLksaevveelkeakelgieve 71 
                                             +ydv++iGgGpgGYvaAira+qlgl++alvek++lGG+Cln+GCiPtKalL+ aev++++ +a++lg++++
  lcl|FitnessBrowser__Koxy:BWI76_RS14145   4 KYDVLIIGGGPGGYVAAIRAGQLGLRTALVEKQHLGGICLNWGCIPTKALLHGAEVAHTIAHADRLGFSLS 74 
                                             59********************************************************************* PP

                               TIGR01350  72 nvkldlekllerkekvvkklvgGvkaLlkknkvevikGeaklldkkevevkkekke.kkleakniiiAtGs 141
                                             +v++dl+kl++ +++v+++l+gGv++Llkkn+v+vi G+a+l++k++v+v++ ++e + ++a+++i+AtG+
  lcl|FitnessBrowser__Koxy:BWI76_RS14145  75 EVSFDLQKLVQFSRAVSQQLTGGVEYLLKKNGVTVIAGTARLRGKGQVTVADPQGEeRDYRADHVILATGA 145
                                             ***************************************************99888689************ PP

                               TIGR01350 142 eprelplkleedekvvitseealelkevpeslvivGgGviGvEfasifaklGvkvtvielldrilpaldae 212
                                             +pr+lp+ +e d+++++t+ eal+ +++pesl+i+G+G+iGvEfas++++lG++vt++e + +ilp++dae
  lcl|FitnessBrowser__Koxy:BWI76_RS14145 146 RPRALPG-VEPDGERIWTYFEALQPERLPESLLIIGSGAIGVEFASLYNDLGSNVTLVEQAAQILPVEDAE 215
                                             *******.*************************************************************** PP

                               TIGR01350 213 vskvlkkklkkkgvkiltnakvtevekeedevvveakkk.evetleaekvLvavGrkpnleelgleklgve 282
                                             vs +++k+++++g+++++++ +t+v++++  v++  k +  ++tle+e+vL+a G++pn+e+lgle+lgve
  lcl|FitnessBrowser__Koxy:BWI76_RS14145 216 VSATVRKSFERRGIHVHSQTLLTQVKRTDTGVRCALKTTgAEQTLEVERVLLAAGVQPNVEGLGLEALGVE 286
                                             *********************************7777776779**************************** PP

                               TIGR01350 283 ldergaikvdeelrtnvpgiyaiGDvigklmLAhvAskegvvaaekiagkeks.eidykavPsviytePev 352
                                             ld+ g+ik+d+ +rtnv g+yaiGDv+g++ LAh+As+egv+++e++ag e    ++ ++vP ++y++P+v
  lcl|FitnessBrowser__Koxy:BWI76_RS14145 287 LDR-GFIKTDAACRTNVFGLYAIGDVAGPPCLAHKASHEGVICVETLAGVEGVrPLNCDYVPGCTYARPQV 356
                                             *98.*********************************************999889**************** PP

                               TIGR01350 353 asvGlteeqakeegievkvgkfpfaangkalaleetdGfvkvivdkktgeilGahivgaeaseliselala 423
                                             as+Glte++a+e g  +kvgkf ++ ngkala++et+Gfvk+i+d +tge+lGah+vg++++e i+ + +a
  lcl|FitnessBrowser__Koxy:BWI76_RS14145 357 ASLGLTEAKARETGRPIKVGKFAYQGNGKALASGETEGFVKTIFDAETGELLGAHMVGEQVTEQIQGFGIA 427
                                             *********************************************************************** PP

                               TIGR01350 424 veleltveelaktihpHPtlsEaikeaalaalgkaih 460
                                              +le+t e+l ++i++HPtlsEa++e++laa+g+++h
  lcl|FitnessBrowser__Koxy:BWI76_RS14145 428 HHLEATDESLLSMIFAHPTLSEAMHESILAASGQPLH 464
                                             ***********************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (461 nodes)
Target sequences:                          1  (465 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: 10.72
//
[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