Alignments for a candidate for ilvD in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Marinobacter adhaerens HP15

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase

Query= SwissProt::Q1MIB2
         (612 letters)



>FitnessBrowser__Marino:GFF612
          Length = 597

 Score =  889 bits (2297), Expect = 0.0
 Identities = 440/595 (73%), Positives = 499/595 (83%), Gaps = 2/595 (0%)

Query: 15  MAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEF 74
           MAGAR LWRATGMKD DFGKPIIAV NSFTQFVPGHVHLKDLGQLV REIE+AGGVAKEF
Sbjct: 1   MAGARALWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEF 60

Query: 75  NTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASL 134
           NTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCISNCDKITPGMLMA++
Sbjct: 61  NTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAM 120

Query: 135 RLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDEDVQTIERSACPTCGS 194
           RLNIPT+FVSGGPMEAGK  +    H LDLVDAMV AAD   SDE V+  ER+ACPTCGS
Sbjct: 121 RLNIPTIFVSGGPMEAGKTKL--SEHKLDLVDAMVIAADPNASDEQVEEYERNACPTCGS 178

Query: 195 CSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIVDLARRYYEQDDVKA 254
           CSGMFTANSMNCLTEA+GL+LPGNGS LATH DR++LF++AG  IV+ ARRYYE+DD   
Sbjct: 179 CSGMFTANSMNCLTEAIGLALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASV 238

Query: 255 LPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMADIDALSRRVPCLSKV 314
           LP +IAS  AFENAM +DIAMGGSTNT+LH+LAAA EG + FT+ +ID LSRRVP L KV
Sbjct: 239 LPLSIASMAAFENAMVMDIAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKV 298

Query: 315 APAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDAIDRWDITRTNSETV 374
           AP     HMEDVHRAGGIM ILGEL++GGL+N D PTVH++T+ +A++ WDI R+    V
Sbjct: 299 APNSPKYHMEDVHRAGGIMGILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEV 358

Query: 375 RKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDGGLAVLKGNLAIDGC 434
            +FY+A P GIPTQ AFSQ  RW  LD DRE G IRSVE+ +S +GGLAVL GN+A+DGC
Sbjct: 359 VEFYKAGPAGIPTQTAFSQSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGC 418

Query: 435 IVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRYEGPKGGPGMQEMLY 494
           +VKTAGVDESI  F G ARVFESQD++V  IL++EVK G+VV+IRYEGP+GGPGMQEMLY
Sbjct: 419 VVKTAGVDESIFVFEGKARVFESQDSAVAGILSDEVKPGEVVIIRYEGPRGGPGMQEMLY 478

Query: 495 PTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGLVREGDMIDIDIPNR 554
           PTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL+  GD I IDIPNR
Sbjct: 479 PTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRIDIPNR 538

Query: 555 TISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATSADRGAVRDL 609
           +I++ + + EL  RR  +DAKGW P   R R V+ ALKAYA  ATSAD+GAVRDL
Sbjct: 539 SINVELDQHELDRRREARDAKGWKPELPRDRKVSAALKAYALLATSADKGAVRDL 593


Lambda     K      H
   0.318    0.134    0.391 

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: 1203
Number of extensions: 26
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: 612
Length of database: 597
Length adjustment: 37
Effective length of query: 575
Effective length of database: 560
Effective search space:   322000
Effective search space used:   322000
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 GFF612 HP15_595 (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.10119.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.9e-255  832.4   0.5   9.1e-255  832.2   0.5    1.0  1  lcl|FitnessBrowser__Marino:GFF612  HP15_595 dihydroxy-acid dehydrat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF612  HP15_595 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  832.2   0.5  9.1e-255  9.1e-255       2     542 ..       4     592 ..       3     593 .. 0.99

  Alignments for each domain:
  == domain 1  score: 832.2 bits;  conditional E-value: 9.1e-255
                          TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 
                                        aral++atG+kd d++kPiiav+ns+t++vPghvhlkdl++lv +eie+aGgvakefntiav+DGiamgh+Gm+ys
  lcl|FitnessBrowser__Marino:GFF612   4 ARALWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTIAVDDGIAMGHDGMLYS 79 
                                        79************************************************************************** PP

                          TIGR00110  78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavg 153
                                        LpsreiiaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagktklse  +++d+++a++
  lcl|FitnessBrowser__Marino:GFF612  80 LPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTKLSE--HKLDLVDAMV 153
                                        *************************************************************977..589******* PP

                          TIGR00110 154 eyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkk 229
                                         +a+++ s+e++ee+er+acPt+gsCsG+ftansm+cltea+Gl+lPg+++llat+a++++l+ k+g++ive  ++
  lcl|FitnessBrowser__Marino:GFF612 154 IAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIGLALPGNGSLLATHADREQLFLKAGRQIVENARR 229
                                        **************************************************************************** PP

                          TIGR00110 230 nik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv 298
                                        +++       P +i++ +afena+++d+a+GGstnt+Lhlla+a+e gv ++l+++d+lsr+vP+l+k++P++ k+
  lcl|FitnessBrowser__Marino:GFF612 230 YYEeddasvlPLSIASMAAFENAMVMDIAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKY 305
                                        *************************************************************************998 PP

                          TIGR00110 299 .iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................. 344
                                         +ed+hraGG++++l+el++ gl+++d  tv  kt+ e le+ +++r                             
  lcl|FitnessBrowser__Marino:GFF612 306 hMEDVHRAGGIMGILGELERGGLINTDLPTVHSKTMREALETWDIMRspptevvefykagpagiptqtafsqstrw 381
                                        8*************************************************************************** PP

                          TIGR00110 345 ......vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               ++ +irs++n++++egglavL+Gn+a +G+vvk+agv+e+i +feG+a+vfes++ a+++il+ +vk G
  lcl|FitnessBrowser__Marino:GFF612 382 ptldgdRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKARVFESQDSAVAGILSDEVKPG 457
                                        **88655566****************************************************************** PP

                          TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkiki 490
                                        +vv+iryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+l+e+GD+i+i
  lcl|FitnessBrowser__Marino:GFF612 458 EVVIIRYEGPRGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRI 533
                                        **************************************************************************** PP

                          TIGR00110 491 Dienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542
                                        Di+nr +++e++++el++rr++ ++k++       r+v+ aL++ya l++sadkGav+d
  lcl|FitnessBrowser__Marino:GFF612 534 DIPNRSINVELDQHELDRRREARDAKGWkpelprdRKVSAALKAYALLATSADKGAVRD 592
                                        ***************************999****99*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (597 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: 11.21
//
[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:

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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis