GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Klebsiella michiganensis M5al

Align dihydroxyacid dehydratase (characterized)
to candidate BWI76_RS00975 BWI76_RS00975 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__Koxy:BWI76_RS00975
          Length = 616

 Score = 1177 bits (3044), Expect = 0.0
 Identities = 588/616 (95%), Positives = 607/616 (98%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MPKYRSATTTHGRNMAGARALWRATGMTD DFGKPIIAVVNSFTQFVPGHVHLRDLGKLV
Sbjct: 1   MPKYRSATTTHGRNMAGARALWRATGMTDDDFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSD Q
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDDQ 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAG RIV
Sbjct: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGSRIV 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           ELTKRYYEQ+D SALPRNIA+KAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD
Sbjct: 241 ELTKRYYEQDDASALPRNIANKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGV+GILGEL+RAGLLNRDVKNVLGL+LPQT
Sbjct: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVLGILGELERAGLLNRDVKNVLGLSLPQT 360

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           LEQYD+ +TQD+AVK MFRAGPAGIRTTQAFSQ+CRWDTLDDDRA GCIRSLEHAYSKDG
Sbjct: 361 LEQYDITVTQDEAVKKMFRAGPAGIRTTQAFSQNCRWDTLDDDRAEGCIRSLEHAYSKDG 420

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQD AV+AILGGK+VAGDVVVIRY
Sbjct: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDAAVDAILGGKIVAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPT+FLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGG+I +
Sbjct: 481 EGPKGGPGMQEMLYPTTFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGNIAI 540

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600
           IEDGD+IAIDIPNRGIQLQ+SDAE+AARREAQ+ARGDKAWTPK+RERQVSFALRAYASLA
Sbjct: 541 IEDGDMIAIDIPNRGIQLQLSDAEIAARREAQEARGDKAWTPKDRERQVSFALRAYASLA 600

Query: 601 TSADKGAVRDKSKLGG 616
           TSADKGAVRDKSKLGG
Sbjct: 601 TSADKGAVRDKSKLGG 616


Lambda     K      H
   0.317    0.134    0.386 

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: 1419
Number of extensions: 36
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: 616
Length of database: 616
Length adjustment: 37
Effective length of query: 579
Effective length of database: 579
Effective search space:   335241
Effective search space used:   335241
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 BWI76_RS00975 BWI76_RS00975 (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.9490.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   6.6e-275  898.7   3.4   7.7e-275  898.5   3.4    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS00975  BWI76_RS00975 dihydroxy-acid deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS00975  BWI76_RS00975 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  898.5   3.4  7.7e-275  7.7e-275       2     542 ..      18     610 ..      17     611 .. 0.99

  Alignments for each domain:
  == domain 1  score: 898.5 bits;  conditional E-value: 7.7e-275
                               TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamghe 72 
                                             aral++atG++d+d++kPiiavvns+t++vPghvhl+dl+klv+e+ieaaGgvakefntiav+DGiamgh+
  lcl|FitnessBrowser__Koxy:BWI76_RS00975  18 ARALWRATGMTDDDFGKPIIAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGVAKEFNTIAVDDGIAMGHG 88 
                                             79********************************************************************* PP

                               TIGR00110  73 GmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklseki 143
                                             Gm+ysLpsre+iaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+i+vsGGpmeagktkls++i
  lcl|FitnessBrowser__Koxy:BWI76_RS00975  89 GMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQI 159
                                             *********************************************************************** PP

                               TIGR00110 144 dlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekke 214
                                             +++d+++a+++ a++k+s+++++++ersacPt+gsCsG+ftansm+cltealGls+Pg+++llat+a++k+
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 160 IKLDLVDAMIQGADPKVSDDQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQ 230
                                             *********************************************************************** PP

                               TIGR00110 215 lakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddf 278
                                             l+ ++g rivel+k++++       Pr+i++k+afena+tld+a+GGstntvLhlla+a+ea+++++++d+
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 231 LFLNAGSRIVELTKRYYEqddasalPRNIANKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSDI 301
                                             *********************************************************************** PP

                               TIGR00110 279 drlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.... 344
                                             d+lsrkvP+l+k++Ps++k+ +ed+hraGGv ++l+el+++gll++d+++v+G +l +tle+++++     
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 302 DKLSRKVPQLCKVAPSTQKYhMEDVHRAGGVLGILGELERAGLLNRDVKNVLGLSLPQTLEQYDITVtqde 372
                                             *******************99*******************************************99999** PP

                               TIGR00110 345 ...........................vdqd....virsldnpvkkegglavLkGnlaeeGavvkiagvee 384
                                                                        +d+d    +irsl+++++k+gglavL+Gn+ae+G++vk+agv++
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 373 avkkmfragpagirttqafsqncrwdtLDDDraegCIRSLEHAYSKDGGLAVLYGNFAENGCIVKTAGVDD 443
                                             **************************944445566************************************ PP

                               TIGR00110 385 dilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDG 455
                                             +ilkf+Gpakv+es+++a++ailggk+ +GdvvviryeGPkGgPGm+emL+Pt++l+++GLgk++aLitDG
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 444 SILKFTGPAKVYESQDAAVDAILGGKIVAGDVVVIRYEGPKGGPGMQEMLYPTTFLKSMGLGKACALITDG 514
                                             *********************************************************************** PP

                               TIGR00110 456 rfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea........ 518
                                             rfsGgt+GlsiGhvsPeaa+gG+ia++edGD+i+iDi+nr ++l++s++e+a+rr++++++++        
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 515 RFSGGTSGLSIGHVSPEAASGGNIAIIEDGDMIAIDIPNRGIQLQLSDAEIAARREAQEARGDkawtpkdr 585
                                             ************************************************************999999***** PP

                               TIGR00110 519 .revkgaLakyaklvssadkGavld 542
                                              r+v++aL++ya+l++sadkGav+d
  lcl|FitnessBrowser__Koxy:BWI76_RS00975 586 eRQVSFALRAYASLATSADKGAVRD 610
                                             ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (616 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: 12.79
//
[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