Alignments for a candidate for ilvI in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Derxia gummosa DSM 723

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_051377961.1 H566_RS0103585 acetolactate synthase, large subunit, biosynthetic type

Query= metacyc::MONOMER-18810
         (585 letters)



>NCBI__GCF_000482785.1:WP_051377961.1
          Length = 583

 Score =  810 bits (2093), Expect = 0.0
 Identities = 395/569 (69%), Positives = 464/569 (81%), Gaps = 1/569 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E  GAEI+  ALAEEGV +++GYPGG+VLYIYDE+ KQ  F+HILVRHEQAAVHAAD Y+
Sbjct: 15  EYTGAEIVCRALAEEGVTHLFGYPGGSVLYIYDEIFKQDSFQHILVRHEQAAVHAADAYS 74

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R++ KVGVA+VTSGPGVTNAVTG+ATAY+DSIPMVVI+G VPTHAIG DAFQECD VGIT
Sbjct: 75  RSSNKVGVAIVTSGPGVTNAVTGLATAYMDSIPMVVISGQVPTHAIGSDAFQECDAVGIT 134

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP VKHN LVKDVRDLA  I++AF IA TGRPGPV+VDIPKD++    K+EYP+ ++MRS
Sbjct: 135 RPCVKHNILVKDVRDLAPAIRRAFHIAKTGRPGPVLVDIPKDITIARAKFEYPERVEMRS 194

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           YNP  KGH GQI+KA ALL  AERP IY GGGVVLA+A+  L +LA   G PVT TLMGL
Sbjct: 195 YNPAGKGHLGQIKKAAALLLTAERPMIYAGGGVVLADAAPLLNKLADELGFPVTTTLMGL 254

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           G +     ++VGM GMHG YEANMAMQ+CDVL A+GARFDDRVIGNP HF    RKIIH+
Sbjct: 255 GGYKSGDPKWVGMPGMHGWYEANMAMQHCDVLFAVGARFDDRVIGNPKHFAQNERKIIHV 314

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           D+DPSSISKRVKVD+PIVGN+ +VL+EL+  ++      +   +  W +QI++WR + CL
Sbjct: 315 DVDPSSISKRVKVDVPIVGNLYEVLEELVKLVEQGKTSGQVPKIDAWMKQIDEWRGIKCL 374

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y +S E+IKPQ+VVEK+WE+T GDA + SDVGQHQMWAAQ+Y+FD+PRRW+NSGGLGTM
Sbjct: 375 DYRKSDEVIKPQFVVEKLWEVTGGDAIVTSDVGQHQMWAAQYYRFDKPRRWLNSGGLGTM 434

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           GVGLPYAMG + A P   V  ITGEGSIQM IQELSTC QY    KI  LNN YLGMVRQ
Sbjct: 435 GVGLPYAMGAQLANPGVPVACITGEGSIQMNIQELSTCKQYRLTPKIILLNNRYLGMVRQ 494

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF-RLKDRTVFLD 556
           WQ+I+Y +RYS SYMDALPDFVKL E+YGHVG+RV   +DVEPALREAF + KDR VFLD
Sbjct: 495 WQQIDYGSRYSESYMDALPDFVKLVESYGHVGIRVTNPADVEPALREAFGKHKDRLVFLD 554

Query: 557 FQTDPTENVWPMVQAGKGISEMLLGAEDL 585
           F TD TENVWPMV+AGKG++EMLLG+EDL
Sbjct: 555 FITDQTENVWPMVKAGKGLTEMLLGSEDL 583


Lambda     K      H
   0.319    0.135    0.407 

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: 1093
Number of extensions: 38
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: 585
Length of database: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate WP_051377961.1 H566_RS0103585 (acetolactate synthase, large subunit, biosynthetic type)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# 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/TIGR00118.hmm
# target sequence database:        /tmp/gapView.32462.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-245  799.6   0.1   8.4e-245  799.3   0.1    1.0  1  lcl|NCBI__GCF_000482785.1:WP_051377961.1  H566_RS0103585 acetolactate synt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_051377961.1  H566_RS0103585 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  799.3   0.1  8.4e-245  8.4e-245       2     554 ..      17     577 ..      16     580 .. 0.97

  Alignments for each domain:
  == domain 1  score: 799.3 bits;  conditional E-value: 8.4e-245
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +gaei+ ++l +egv ++fGyPGG+vl iyd+++ ++ ++hilvrheqaa+haad y+r+s kvGv+++
  lcl|NCBI__GCF_000482785.1:WP_051377961.1  17 TGAEIVCRALAEEGVTHLFGYPGGSVLYIYDEIFkQDSFQHILVRHEQAAVHAADAYSRSSNKVGVAIV 85 
                                               79********************************9999******************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPG tn+vtg+atay+ds+P+vv++Gqv+t++iGsdafqe+d +Git+p++kh++lvk+++dl+  +
  lcl|NCBI__GCF_000482785.1:WP_051377961.1  86 TSGPGVTNAVTGLATAYMDSIPMVVISGQVPTHAIGSDAFQECDAVGITRPCVKHNILVKDVRDLAPAI 154
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               ++af+ia+tGrPGPvlvd+Pkd+t a  ++e++e+ve+++y+p  kgh  qikka+ l+ +a++P++++
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 155 RRAFHIAKTGRPGPVLVDIPKDITIARAKFEYPERVEMRSYNPAGKGHLGQIKKAAALLLTAERPMIYA 223
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgGv+ a+a   l++la++l  pvtttl+GlG++++ +p+ +gm GmhG +ean+a++++d+l+avGar
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 224 GGGVVLADAAPLLNKLADELGFPVTTTLMGLGGYKSGDPKWVGMPGMHGWYEANMAMQHCDVLFAVGAR 292
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.W 339
                                               fddrv gn ++fa++  kiih+d+dP++i+k vkvd+pivG+  +vleel+k +++     +  +++ W
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 293 FDDRVIGNPKHFAQNErKIIHVDVDPSSISKRVKVDVPIVGNLYEVLEELVKLVEQGktsgQVPKIDaW 361
                                               *************87527**********************************9998756664444456* PP

                                 TIGR00118 340 lekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgG 408
                                               +++i+ew+  ++l + +++e ikPq v+++l++++ ++aivt+dvGqhqmwaaq+y+++kpr++++sgG
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 362 MKQIDEWRGIKCLDYRKSDEVIKPQFVVEKLWEVTGGDAIVTSDVGQHQMWAAQYYRFDKPRRWLNSGG 430
                                               ********************************************************************* PP

                                 TIGR00118 409 lGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelf 477
                                               lGtmG GlP a+Ga++a+p   v ++tG+gs+qmn+qelst+++y +  ki++lnn++lGmv+qWq++ 
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 431 LGTMGVGLPYAMGAQLANPGVPVACITGEGSIQMNIQELSTCKQYRLTPKIILLNNRYLGMVRQWQQID 499
                                               ********************************************************************* PP

                                 TIGR00118 478 yeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPmv 544
                                               y  ryse+++ + lpdfvkl e+yG++gir+++p+++e +l+ea+ ++  ++v+ld+  d++e+v+Pmv
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 500 YGSRYSESYMDA-LPDFVKLVESYGHVGIRVTNPADVEPALREAFGKHkdRLVFLDFITDQTENVWPMV 567
                                               ***********5.*******************************97654599***************** PP

                                 TIGR00118 545 apGagldelv 554
                                                 G+gl+e++
  lcl|NCBI__GCF_000482785.1:WP_051377961.1 568 KAGKGLTEML 577
                                               ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (583 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: 11.24
//
[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