GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pontibacter ramchanderi LP43

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_101446604.1 BD749_RS13355 dihydroxy-acid dehydratase

Query= BRENDA::A0A481UJA7
         (614 letters)



>NCBI__GCF_002846395.1:WP_101446604.1
          Length = 573

 Score =  664 bits (1714), Expect = 0.0
 Identities = 329/555 (59%), Positives = 411/555 (74%), Gaps = 1/555 (0%)

Query: 59  LNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVK 118
           LNKYS   T+  S   SQA+L G GLS EDL KP +GI S  ++GNTCNMHL  L++ VK
Sbjct: 4   LNKYSRIYTQDDSLPASQAMLMGAGLSAEDLRKPFVGICSTGFDGNTCNMHLNDLADEVK 63

Query: 119 EGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPG 178
            GV + GMVG RFNTIGVSD I+ GT+GM YSL SR++IADSIET+  A  YD    + G
Sbjct: 64  RGVNKQGMVGLRFNTIGVSDGITNGTQGMNYSLVSREIIADSIETITGAHNYDALACVVG 123

Query: 179 CDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRK 238
           CDKNMPG++MAM RLNRP++MVYGGTIK G + G   +I+S F+AYG+ +NG +S+ED +
Sbjct: 124 CDKNMPGSLMAMARLNRPALMVYGGTIKGGEFKGEKLNIVSCFEAYGKKLNGQLSEEDYR 183

Query: 239 NVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLEL 298
            ++ N+CPG GACGGMYTANTMASA EA+GM +P+SSS PA +  K +EC   G+YLL L
Sbjct: 184 GIIRNACPGPGACGGMYTANTMASAAEALGMSVPFSSSSPAVSQSKKEECLGTGEYLLRL 243

Query: 299 LKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVP 358
           L+MDLKPQ+I+  ++  NA+V++  LGGSTNAVLHLI IA + G+ L+L DFQ VS+ VP
Sbjct: 244 LEMDLKPQDILVREAFENALVLITVLGGSTNAVLHLIAIAHAAGVPLSLRDFQAVSNRVP 303

Query: 359 FLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEG 418
            LADLKPSGKY+MED+  +GG PAV++ LL  G + GD LTVTGKT+AEN+    PL E 
Sbjct: 304 VLADLKPSGKYLMEDLSTLGGVPAVMKTLLNEGLITGDLLTVTGKTVAENLAGVKPLGEE 363

Query: 419 QDIIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAISE 478
           QD++RPL NPIK  GHIQ L GNLAP+G+VAKI+GKEGL F GPA+VF  EE +   I+ 
Sbjct: 364 QDLLRPLSNPIKADGHIQTLYGNLAPKGAVAKISGKEGLTFEGPAIVFNSEEELNQGIAT 423

Query: 479 NPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVVG 538
             +   G+VVVIR  GPKGGPGMPEML PTSAIMGAGLG   AL+TDGRFSGG+HGFV+G
Sbjct: 424 GKI-VAGQVVVIRYVGPKGGPGMPEMLKPTSAIMGAGLGDKVALITDGRFSGGTHGFVIG 482

Query: 539 HICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLYK 598
           H+CPEA +GG + LV +GD I ++  +  I + V +  ++ RR  W  P  K   GVL K
Sbjct: 483 HVCPEAYDGGTLALVEDGDWISLNANKNTIHLHVEEAVLDLRRDKWQQPAPKVEKGVLLK 542

Query: 599 YIKNVQSASRGCVTD 613
           YI+ V  ASRGC+TD
Sbjct: 543 YIRTVSDASRGCITD 557


Lambda     K      H
   0.316    0.135    0.401 

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: 1102
Number of extensions: 48
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: 614
Length of database: 573
Length adjustment: 37
Effective length of query: 577
Effective length of database: 536
Effective search space:   309272
Effective search space used:   309272
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: 53 (25.0 bits)

Align candidate WP_101446604.1 BD749_RS13355 (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.673308.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.4e-219  714.8   2.7     4e-219  714.6   2.7    1.0  1  NCBI__GCF_002846395.1:WP_101446604.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101446604.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.6   2.7    4e-219    4e-219       2     542 ..      20     557 ..      19     558 .. 1.00

  Alignments for each domain:
  == domain 1  score: 714.6 bits;  conditional E-value: 4e-219
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           ++a+l  +Gl+ edl kP+++++++  + + +++hl+dla+ vk+++++ G v  +fnti+vsDGi+ g++Gm
  NCBI__GCF_002846395.1:WP_101446604.1  20 SQAMLMGAGLSAEDLRKPFVGICSTGFDGNTCNMHLNDLADEVKRGVNKQGMVGLRFNTIGVSDGITNGTQGM 92 
                                           79*********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysL+sreiiaDs+et+  ah +Dal ++  CDk++PG lma++rln+Pa++v+GG+++ g++k +ek+++v+
  NCBI__GCF_002846395.1:WP_101446604.1  93 NYSLVSREIIADSIETITGAHNYDALACVVGCDKNMPGSLMAMARLNRPALMVYGGTIKGGEFK-GEKLNIVS 164
                                           ****************************************************************.9******* PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                            fea+g+  +g+lsee+ + i r+acP++g+C+G++tan+ma+++ealG+s+P ss+++a+s+ kke +  +g
  NCBI__GCF_002846395.1:WP_101446604.1 165 CFEAYGKKLNGQLSEEDYRGIIRNACPGPGACGGMYTANTMASAAEALGMSVPFSSSSPAVSQSKKEECLGTG 237
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkP 293
                                           +++  l++ ++kP+dil +eafena++l+ +lGGstn+vLhl+aia+ agv lsl df+ +s++vP+la+lkP
  NCBI__GCF_002846395.1:WP_101446604.1 238 EYLLRLLEMDLKPQDILVREAFENALVLITVLGGSTNAVLHLIAIAHAAGVPLSLRDFQAVSNRVPVLADLKP 310
                                           ************************************************************************* PP

                             TIGR00110 294 sgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavL 366
                                           sgk+++edl   GGv+av+k+l +egl+  d ltvtGkt+ae+l+ vk l ++qd++r+l+np+k++g+++ L
  NCBI__GCF_002846395.1:WP_101446604.1 311 SGKYLMEDLSTLGGVPAVMKTLLNEGLITGDLLTVTGKTVAENLAGVKPLGEEQDLLRPLSNPIKADGHIQTL 383
                                           ************************************************************************* PP

                             TIGR00110 367 kGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439
                                           +Gnla++Gav+ki+g+e   l+feGpa vf+seee  ++i +gk+ +G+vvviry GPkGgPGm+emL+Ptsa
  NCBI__GCF_002846395.1:WP_101446604.1 384 YGNLAPKGAVAKISGKEG--LTFEGPAIVFNSEEELNQGIATGKIVAGQVVVIRYVGPKGGPGMPEMLKPTSA 454
                                           ******************..9**************************************************** PP

                             TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrak 512
                                           ++g+GLg+kvaLitDGrfsGgt+G++iGhv Pea+ gG++alvedGD i++++++++++l+v+e+ l+ rr+k
  NCBI__GCF_002846395.1:WP_101446604.1 455 IMGAGLGDKVALITDGRFSGGTHGFVIGHVCPEAYDGGTLALVEDGDWISLNANKNTIHLHVEEAVLDLRRDK 527
                                           ************************************************************************* PP

                             TIGR00110 513 akkkearevkgaLakyaklvssadkGavld 542
                                           ++++ ++  kg+L ky + vs a++G+++d
  NCBI__GCF_002846395.1:WP_101446604.1 528 WQQPAPKVEKGVLLKYIRTVSDASRGCITD 557
                                           ***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (573 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.51
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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