Alignments for a candidate for ilvD in Mesorhizobium ciceri WSM1271

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Mesorhizobium ciceri WSM1271

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate YP_004142653.1 Mesci_3483 dihydroxy-acid dehydratase

Query= BRENDA::Q97UB2
         (558 letters)



>NCBI__GCF_000185905.1:YP_004142653.1
          Length = 574

 Score =  539 bits (1389), Expect = e-157
 Identities = 274/558 (49%), Positives = 374/558 (67%), Gaps = 5/558 (0%)

Query: 3   AKLNSPSRYH--GIYNAPHRAFLRSVGLTDEEIGKPLVAIATAWSEAGPCNFHTLALARV 60
           +K   PSRY   G   APHR++L ++GL+  EI +PLV +A+ W+EA PCN   +  A+V
Sbjct: 7   SKAKLPSRYVTVGPARAPHRSYLYAMGLSAAEIAQPLVGVASCWNEAAPCNISLMRQAQV 66

Query: 61  AKEGTKEAGLSPLAFPTMVVNDNIGMGSEGMRYSLVSRDLIADMVEAQFNAHAFDGLVGI 120
            K+G   A  +P  F T+ V D I MG +GM+ SLVSR++IAD VE     H +D LVG+
Sbjct: 67  VKKGVAAASGTPREFCTITVTDGIAMGHQGMKSSLVSREVIADSVELTMRGHCYDALVGL 126

Query: 121 GGCDKTTPGILMAMARLNVPSIYIYGGSAEPGYFMGKRLTIEDVHEAIGAYLAKRITENE 180
            GCDK+ PG++MAM RLNVPSI+IYGGS  PG + G+++T++DV EA+G +    I+++E
Sbjct: 127 AGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGSYRGRQITVQDVFEAVGQHSVGAISDDE 186

Query: 181 LYEIEKRAHPTLGTCSGLFTANTMGSMSEALGMALPGSASPTATSSRRVMYVKETGKALG 240
           L EIE+ A P+ G+C   FTANTM +++EA+G+ALP S    A    R  +   +G+ + 
Sbjct: 187 LLEIEQVACPSAGSCGAQFTANTMATVAEAIGLALPYSCGAPAPYEMRDRFNFASGEKIM 246

Query: 241 SLIENGIKSREILTFEAFENAITTLMAMGGSTNAVLHLLAIAYEAGVKLTLDDFNRISKR 300
            LI   I+ R+I+T +A ENA T + A GGSTNA LHL AIA+EAG+K  L D  +I ++
Sbjct: 247 ELIARNIRPRDIVTLKALENAATVVSATGGSTNAALHLPAIAHEAGIKFDLFDVAKIFEK 306

Query: 301 TPYIASMKPGGDYVMADLDEVGGVPVVLKKLLDAGLLHGDVLTVTGKTMKQNLEQYKYPN 360
           TPYIA +KPGG YV  D+ E GG+P+++K LLD G LHGD +TVTG+T+ +N++   +  
Sbjct: 307 TPYIADLKPGGKYVAKDMFEAGGIPLLMKTLLDHGYLHGDCMTVTGRTLAENMQHVVWNE 366

Query: 361 VPHSHIVRDVKNPIKPRGGIVILKGSLAPEGAVIKVAATNVVKFEGKAKVYNSEDDAFKG 420
             H  +VR    PI   GG+V LKG+LAPEGA++KVA    +KF G A+ ++SE++ F+ 
Sbjct: 367 --HQDVVRPANRPITQTGGVVGLKGNLAPEGAIVKVAGMAELKFSGPARCFDSEEECFEA 424

Query: 421 VQSGEVSEGEVVIIRYEGPKGAPGMPEMLRVTAAIMGAGL-NNVALVTDGRFSGATRGPM 479
           V      EGEV++IRYEGP+G PGM EML  TAA+ G G+   VAL+TDGRFSGATRG  
Sbjct: 425 VTHRNYREGEVLVIRYEGPRGGPGMREMLSTTAALYGQGMGGKVALITDGRFSGATRGFC 484

Query: 480 VGHVAPEAMVGGPIAIVEDGDTIVIDVESERLDLKLSEEEIKNRLKRWSPPSPRYKSGLL 539
           +GHV PEA VGGPI ++ DGD I ID  +  +D+ LS+ E+  R K W   +  Y+SG +
Sbjct: 485 IGHVGPEAAVGGPIGLLRDGDVISIDAVNGTIDVALSDSELAARAKTWKARATDYQSGAI 544

Query: 540 AKYASLVSQASMGAVTRP 557
            KYA  V  A  GAVT P
Sbjct: 545 WKYAQTVGPARDGAVTHP 562


Lambda     K      H
   0.316    0.134    0.383 

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: 838
Number of extensions: 35
Number of successful extensions: 3
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: 558
Length of database: 574
Length adjustment: 36
Effective length of query: 522
Effective length of database: 538
Effective search space:   280836
Effective search space used:   280836
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 YP_004142653.1 Mesci_3483 (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.24228.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-212  693.4   1.9   1.1e-212  693.2   1.9    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004142653.1  Mesci_3483 dihydroxy-acid dehydr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004142653.1  Mesci_3483 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.2   1.9  1.1e-212  1.1e-212       1     541 [.      24     560 ..      24     562 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.2 bits;  conditional E-value: 1.1e-212
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               ++r+ l+a+Gl+ +++ +P+++v+++++e +P++++l   a++vk+++ aa g++ ef ti+v+DGiam
  lcl|NCBI__GCF_000185905.1:YP_004142653.1  24 PHRSYLYAMGLSAAEIAQPLVGVASCWNEAAPCNISLMRQAQVVKKGVAAASGTPREFCTITVTDGIAM 92 
                                               699****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gmk sL+sre+iaDsve  +++h++Dalv ++ CDk +PGm+ma++rln+P+i+++GG++ +g ++
  lcl|NCBI__GCF_000185905.1:YP_004142653.1  93 GHQGMKSSLVSREVIADSVELTMRGHCYDALVGLAGCDKSLPGMMMAMVRLNVPSIFIYGGSILPGSYR 161
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                +++i++ dvfeavg+ + g +s++el eie++acP+agsC+  ftan+ma+++ea+Gl+lP+s  ++a
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 162 -GRQITVQDVFEAVGQHSVGAISDDELLEIEQVACPSAGSCGAQFTANTMATVAEAIGLALPYSCGAPA 229
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                                 + + ++   sg++i+el+ +ni+Prdi+t +a+ena t++ a+GGstn+ Lhl+aia+eag+k++l 
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 230 PYEMRDRFNFASGEKIMELIARNIRPRDIVTLKALENAATVVSATGGSTNAALHLPAIAHEAGIKFDLF 298
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               d+ ++ +k+P +a+lkP+gk+v +d+ +aGG++ ++k+l  +g+lh d++tvtG+tlae++++v  + +
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 299 DVAKIFEKTPYIADLKPGGKYVAKDMFEAGGIPLLMKTLLDHGYLHGDCMTVTGRTLAENMQHVVWN-E 366
                                               *************************************************************999888.9 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               +qdv+r+ + p++++gg+  LkGnla+eGa+vk+ag++e  lkf Gpa+ f+seee+ ea+ +++ +eG
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 367 HQDVVRPANRPITQTGGVVGLKGNLAPEGAIVKVAGMAE--LKFSGPARCFDSEEECFEAVTHRNYREG 433
                                               ***************************************..**************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               +v+viryeGP+GgPGmremL  t+al g G+g kvaLitDGrfsG+trG++iGhv Peaa+gG+i+l++
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 434 EVLVIRYEGPRGGPGMREMLSTTAALYGQGMGGKVALITDGRFSGATRGFCIGHVGPEAAVGGPIGLLR 502
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541
                                               dGD i+iD+ n ++d+++s+ ela+r +++k++ + +++ga+ kya+ v  a +Gav+
  lcl|NCBI__GCF_000185905.1:YP_004142653.1 503 DGDVISIDAVNGTIDVALSDSELAARAKTWKARATDYQSGAIWKYAQTVGPARDGAVT 560
                                               ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (574 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.93
//
[ok]

This GapMind analysis is from Apr 10 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