Alignments for a candidate for ilvD in Lacinutrix algicola AKS293

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Lacinutrix algicola AKS293

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_055434896.1 ASC41_RS01600 dihydroxy-acid dehydratase

Query= BRENDA::A0A481UJA7
         (614 letters)



>NCBI__GCF_001418085.1:WP_055434896.1
          Length = 559

 Score =  689 bits (1778), Expect = 0.0
 Identities = 344/557 (61%), Positives = 431/557 (77%), Gaps = 1/557 (0%)

Query: 58  KLNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAV 117
           +LNKYS  +T+  +Q  +QA+LH +GL+ ED  KP IGI+S  YEGN CNMHL  L++ V
Sbjct: 3   QLNKYSKTVTQDPTQPAAQAMLHAIGLTKEDFFKPIIGIASTGYEGNPCNMHLNDLAKLV 62

Query: 118 KEGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIP 177
           KEG K   ++G  FNTIGVSD ISMGT GM YSL SRD+IADS+ETV+ A  YDG I++ 
Sbjct: 63  KEGTKNKDIIGLIFNTIGVSDGISMGTPGMRYSLPSRDIIADSMETVVQAMSYDGLITVV 122

Query: 178 GCDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDR 237
           GCDKNMPG ++AM RLNRPS++VYGGTI  G +NG   D++SAF+A+G  V G++ + + 
Sbjct: 123 GCDKNMPGALIAMIRLNRPSVLVYGGTIDSGCHNGQKLDVVSAFEAWGSKVAGTMEETEY 182

Query: 238 KNVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLE 297
           +N+V  +CPGAGACGGMYTANTMASAIEA+GM LP++SS PA +  K +E   AG+ L  
Sbjct: 183 QNIVEKACPGAGACGGMYTANTMASAIEALGMTLPFNSSNPALSGAKKEESVRAGEALRL 242

Query: 298 LLKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEV 357
           LL+ D+KP +IIT +SL NA+ +V  LGGSTNAVLH + IAR+  ++ TL+DFQ +SD  
Sbjct: 243 LLEKDIKPSDIITRKSLENAVRLVTILGGSTNAVLHFLAIARAAQIDFTLKDFQDISDNT 302

Query: 358 PFLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSE 417
           PFLADLKPSGKY+MEDVH +GG PAV++YLL+ G L GDCLTVTGKT+AEN+ +   L+E
Sbjct: 303 PFLADLKPSGKYLMEDVHAVGGIPAVMKYLLKKGMLHGDCLTVTGKTIAENLLDVADLTE 362

Query: 418 GQDIIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAIS 477
           GQD+I+ +E+PIK +GH+++L GNLA EGSVAKITGKEGL F G A VFEGE A    I 
Sbjct: 363 GQDVIKSIEDPIKISGHLRMLYGNLATEGSVAKITGKEGLKFKGKAKVFEGEYAANDGIR 422

Query: 478 ENPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVV 537
           +  +  KG VVVIR EGPKGGPGMPEML PT+AIMGAGLGKD AL+TDGRFSGG+HGFVV
Sbjct: 423 DGLVE-KGDVVVIRYEGPKGGPGMPEMLKPTAAIMGAGLGKDVALITDGRFSGGTHGFVV 481

Query: 538 GHICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLY 597
           GHI PEAQEGG + LV++GD+I ID     I ++V+DQE+++RR++W  P  K   GVLY
Sbjct: 482 GHITPEAQEGGNLALVKDGDVITIDAETNSIVLEVSDQELQKRRQSWKAPDLKFKRGVLY 541

Query: 598 KYIKNVQSASRGCVTDE 614
           KY K V SAS+GCVTDE
Sbjct: 542 KYAKTVSSASKGCVTDE 558


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: 1033
Number of extensions: 39
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: 559
Length adjustment: 37
Effective length of query: 577
Effective length of database: 522
Effective search space:   301194
Effective search space used:   301194
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_055434896.1 ASC41_RS01600 (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.33351.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-226  738.1   6.7   3.5e-226  737.9   6.7    1.0  1  NCBI__GCF_001418085.1:WP_055434896.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001418085.1:WP_055434896.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  737.9   6.7  3.5e-226  3.5e-226       2     542 ..      20     557 ..      19     558 .. 0.99

  Alignments for each domain:
  == domain 1  score: 737.9 bits;  conditional E-value: 3.5e-226
                             TIGR00110   2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 
                                           a+a+l+a+Gl++ed+ kPii+++++  e +P+++hl+dlaklvke+ ++   +   fnti+vsDGi+mg+ Gm
  NCBI__GCF_001418085.1:WP_055434896.1  20 AQAMLHAIGLTKEDFFKPIIGIASTGYEGNPCNMHLNDLAKLVKEGTKNKDIIGLIFNTIGVSDGISMGTPGM 92 
                                           79*********************************************************************** PP

                             TIGR00110  75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147
                                           +ysLpsr+iiaDs+etvv+a  +D+l+++  CDk++PG+l+a++rln+P+++v+GG++ +g  + ++k+d+v+
  NCBI__GCF_001418085.1:WP_055434896.1  93 RYSLPSRDIIADSMETVVQAMSYDGLITVVGCDKNMPGALIAMIRLNRPSVLVYGGTIDSGCHN-GQKLDVVS 164
                                           *************************************************************999.9******* PP

                             TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
                                           +fea g+  ag ++e e ++i++ acP+ag+C+G++tan+ma++ ealG++lP +s+ +a s  kke   ++g
  NCBI__GCF_001418085.1:WP_055434896.1 165 AFEAWGSKVAGTMEETEYQNIVEKACPGAGACGGMYTANTMASAIEALGMTLPFNSSNPALSGAKKEESVRAG 237
                                           ************************************************************************* PP

                             TIGR00110 221 krivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkP 293
                                           + +  l++k+ikP+di+t++++ena+ l+ +lGGstn+vLh laia+ a+++++l+df+ +s+++P la+lkP
  NCBI__GCF_001418085.1:WP_055434896.1 238 EALRLLLEKDIKPSDIITRKSLENAVRLVTILGGSTNAVLHFLAIARAAQIDFTLKDFQDISDNTPFLADLKP 310
                                           ************************************************************************* PP

                             TIGR00110 294 sgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavL 366
                                           sgk+++ed+h++GG++av+k+l k+g+lh d+ltvtGkt+ae+l +v  l+++qdvi+s+++p+k  g+l++L
  NCBI__GCF_001418085.1:WP_055434896.1 311 SGKYLMEDVHAVGGIPAVMKYLLKKGMLHGDCLTVTGKTIAENLLDVADLTEGQDVIKSIEDPIKISGHLRML 383
                                           **************************************************9********************** PP

                             TIGR00110 367 kGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439
                                           +Gnla+eG+v+ki+g+e   lkf+G+akvfe e +a ++i +g v++GdvvviryeGPkGgPGm+emL+Pt+a
  NCBI__GCF_001418085.1:WP_055434896.1 384 YGNLATEGSVAKITGKEG--LKFKGKAKVFEGEYAANDGIRDGLVEKGDVVVIRYEGPKGGPGMPEMLKPTAA 454
                                           ******************..***************************************************** PP

                             TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrak 512
                                           ++g+GLgk+vaLitDGrfsGgt+G+++Gh++Pea egG++alv+dGD i+iD+e + + levs++el++rr++
  NCBI__GCF_001418085.1:WP_055434896.1 455 IMGAGLGKDVALITDGRFSGGTHGFVVGHITPEAQEGGNLALVKDGDVITIDAETNSIVLEVSDQELQKRRQS 527
                                           ************************************************************************* PP

                             TIGR00110 513 akkkearevkgaLakyaklvssadkGavld 542
                                           +k+++ + ++g+L kyak vssa+kG+v+d
  NCBI__GCF_001418085.1:WP_055434896.1 528 WKAPDLKFKRGVLYKYAKTVSSASKGCVTD 557
                                           ****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (559 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: 00:00:00.01
# Mc/sec: 16.07
//
[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:

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 2024 update 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 original 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