GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Caulobacter crescentus NA1000

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>FitnessBrowser__Caulo:CCNA_03139
          Length = 617

 Score = 1224 bits (3168), Expect = 0.0
 Identities = 617/617 (100%), Positives = 617/617 (100%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV
Sbjct: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD
Sbjct: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA
Sbjct: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG
Sbjct: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY
Sbjct: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL
Sbjct: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600
           VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT
Sbjct: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600

Query: 601 TNAARGAVRDVSQIERG 617
           TNAARGAVRDVSQIERG
Sbjct: 601 TNAARGAVRDVSQIERG 617


Lambda     K      H
   0.318    0.134    0.395 

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: 1577
Number of extensions: 38
Number of successful extensions: 1
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: 617
Length of database: 617
Length adjustment: 37
Effective length of query: 580
Effective length of database: 580
Effective search space:   336400
Effective search space used:   336400
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate CCNA_03139 CCNA_03139 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# 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.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.13662.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-248  811.0   3.5   2.8e-248  810.8   3.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03139  CCNA_03139 dihydroxy-acid dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03139  CCNA_03139 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  810.8   3.5  2.8e-248  2.8e-248       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 810.8 bits;  conditional E-value: 2.8e-248
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ar l++atG+kded++kPiiav+ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamgh+Gm
  lcl|FitnessBrowser__Caulo:CCNA_03139  18 ARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHGGM 90 
                                           689********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+++  ki  +d
  lcl|FitnessBrowser__Caulo:CCNA_03139  91 LYSLPSRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALD 163
                                           ************************************************************************* PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +++a++ +a++  s+ee+e+ie+ acPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+k++g
  lcl|FitnessBrowser__Caulo:CCNA_03139 164 LVDAMVVAADDSYSDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAG 236
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286
                                           + +v+l+++ ++       Pr i+t++afena++ld+a+GGstntvLhlla+a+e g+++s+ d+drlsr+vP
  lcl|FitnessBrowser__Caulo:CCNA_03139 237 RVVVDLCQRWYEqedatalPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVP 309
                                           ***********99************************************************************ PP

                             TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344
                                           +l+k++P+ + v +ed+hraGGv+a+l+el++ gl++    tv   t++e l++ ++ r              
  lcl|FitnessBrowser__Caulo:CCNA_03139 310 CLSKVAPAKSDVhMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEALARWDIGRtnsqiaheffkaap 382
                                           ********88888********************************************999************* PP

                             TIGR00110 345 .....................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396
                                                                 ++ virs+++p++k+gglavL+Gnla+eG++vk+agv+e+il+f+G+a+vf
  lcl|FitnessBrowser__Caulo:CCNA_03139 383 ggkptqvafsqaarweeldldRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVF 455
                                           *****************99665666************************************************ PP

                             TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhv 469
                                           es+++a+ +ilgg+vk+G+vvviryeGPkGgPGm+emL+Pt++l++ GLg ++aL+tDGrfsGgt+GlsiGhv
  lcl|FitnessBrowser__Caulo:CCNA_03139 456 ESQDAAVSGILGGQVKAGEVVVIRYEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHV 528
                                           ************************************************************************* PP

                             TIGR00110 470 sPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyaklvs 533
                                           sPea egG ialve GD i iDi+ r + levs++ la+rr+++ ++++         r    aL++ya + +
  lcl|FitnessBrowser__Caulo:CCNA_03139 529 SPEAGEGGLIALVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKdawtplnrkRDLTPALRAYAAMTT 601
                                           ********************************************99999999****9999999********** PP

                             TIGR00110 534 sadkGavld 542
                                           +a +Gav+d
  lcl|FitnessBrowser__Caulo:CCNA_03139 602 NAARGAVRD 610
                                           *******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (617 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 0.02s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.84
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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