Alignments for a candidate for ilvI in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Allochromatium vinosum DSM 180

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012970167.1 ALVIN_RS04700 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000025485.1:WP_012970167.1
          Length = 587

 Score =  775 bits (2001), Expect = 0.0
 Identities = 383/568 (67%), Positives = 450/568 (79%), Gaps = 3/568 (0%)

Query: 15  AAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAAD 74
           AAPE+ GAEI++ AL +EGVE V+GYPGG+VL+IYD L KQ   +HILVRHEQAA HAAD
Sbjct: 11  AAPELSGAEIVIQALVDEGVELVFGYPGGSVLHIYDALFKQGSLKHILVRHEQAAAHAAD 70

Query: 75  GYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTV 134
           GYARATGK GV LVTSGPG TNAVTGIATAY+DSIPMVV+TG VPT  IG DAFQE DTV
Sbjct: 71  GYARATGKCGVCLVTSGPGATNAVTGIATAYMDSIPMVVLTGQVPTPFIGSDAFQEVDTV 130

Query: 135 GITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACK--YEYPKS 192
           GITRP VKHNFLVKDVRDLA TI+KAF IA TGRPGPVV+DIPKDV+    K  Y YP+ 
Sbjct: 131 GITRPCVKHNFLVKDVRDLALTIRKAFHIATTGRPGPVVIDIPKDVTDPNIKIPYVYPRE 190

Query: 193 IDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTN 252
           I +RSYNPV KGH GQIRKAV L+  A+RP  YTGGGVVL + S +L +L   TG P+T+
Sbjct: 191 IKLRSYNPVEKGHLGQIRKAVDLMLAAKRPVFYTGGGVVLGDGSAQLTELVKATGFPITS 250

Query: 253 TLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQAR 312
           TLMGLGAFP T  QF+GMLGMHGTYEANMAM   DVLIAIGARFDDRV G   HF   A+
Sbjct: 251 TLMGLGAFPMTDPQFLGMLGMHGTYEANMAMHETDVLIAIGARFDDRVTGKIEHFCPHAQ 310

Query: 313 KIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWR 372
            IIHID+DPSSISK VKVD+PIVG V  VL +++   +    K    AL  WW +I +WR
Sbjct: 311 -IIHIDVDPSSISKNVKVDVPIVGQVASVLADMLRLYREQQPKSPVNALGDWWAKIGEWR 369

Query: 373 SVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432
           ++DCLKY  S+E IKPQ+ VE ++++T G+ ++ SDVGQHQM+AAQFY FD+PRRWINSG
Sbjct: 370 ALDCLKYPTSAEAIKPQFAVETLYKVTNGELYLASDVGQHQMFAAQFYPFDKPRRWINSG 429

Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492
           GLGTMG GLP A+G + A PE +V  I+G+ SI MCIQEL+TC QY  P+K+  LNNGY+
Sbjct: 430 GLGTMGYGLPAAIGAQLAHPEAQVACISGDASILMCIQELATCQQYRLPIKVVLLNNGYM 489

Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552
           GMVRQWQE+ Y++RYSHSY+DALPDFVKLAE++GHVGMRVE+   +E A+REAF ++DR 
Sbjct: 490 GMVRQWQELFYESRYSHSYVDALPDFVKLAESFGHVGMRVERPEHLEDAMREAFAMRDRF 549

Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLL 580
           VFLD   DPTENV+PM+ AGKG  EM L
Sbjct: 550 VFLDVIVDPTENVYPMIAAGKGHHEMQL 577


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: 1016
Number of extensions: 28
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: 585
Length of database: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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_012970167.1 ALVIN_RS04700 (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.25123.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-265  866.6   0.0   4.1e-265  866.4   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970167.1  ALVIN_RS04700 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970167.1  ALVIN_RS04700 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  866.4   0.0  4.1e-265  4.1e-265       1     554 [.      15     576 ..      15     579 .. 0.98

  Alignments for each domain:
  == domain 1  score: 866.4 bits;  conditional E-value: 4.1e-265
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei++++l +egve vfGyPGG+vl+iydal+ ++ l+hilvrheqaaahaadGyara+Gk Gv+l
  lcl|NCBI__GCF_000025485.1:WP_012970167.1  15 LSGAEIVIQALVDEGVELVFGYPGGSVLHIYDALFkQGSLKHILVRHEQAAAHAADGYARATGKCGVCL 83 
                                               68*********************************9999****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgiatay+ds+P+vvltGqv+t  iGsdafqe+d +Git+p++kh+flvk+++dl+ +
  lcl|NCBI__GCF_000025485.1:WP_012970167.1  84 VTSGPGATNAVTGIATAYMDSIPMVVLTGQVPTPFIGSDAFQEVDTVGITRPCVKHNFLVKDVRDLALT 152
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204
                                               +++af+ia+tGrPGPv++d+Pkdvt+++i++++   ++++l++y+p  kgh  qi+ka++l+ +ak+Pv
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 153 IRKAFHIATTGRPGPVVIDIPKDVTDPNIKIPYVypREIKLRSYNPVEKGHLGQIRKAVDLMLAAKRPV 221
                                               ******************************9998889******************************** PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                                + GgGv+ +++s++l+el++++  p+t+tl+GlGafp ++p++lgmlGmhGt+ean+a++e+d+lia+
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 222 FYTGGGVVLGDGSAQLTELVKATGFPITSTLMGLGAFPMTDPQFLGMLGMHGTYEANMAMHETDVLIAI 290
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrvtg++++f+p+a+iihid+dP++i+knvkvd+pivG++ +vl+++l+  +e+      +   
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 291 GARFDDRVTGKIEHFCPHAQIIHIDVDPSSISKNVKVDVPIVGQVASVLADMLRLYREQqpksPVNALG 359
                                               ******************************************************999985543222233 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfits 406
                                                W++ki ew++  +lk+ ++ e+ikPq  +++l+k++++e ++++dvGqhqm+aaqfy+++kpr++i+s
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 360 dWWAKIGEWRALDCLKYPTSAEAIKPQFAVETLYKVTNGELYLASDVGQHQMFAAQFYPFDKPRRWINS 428
                                               5******************************************************************** PP

                                 TIGR00118 407 gGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqe 475
                                               gGlGtmG+GlPaa+Ga++a+pe++v +++Gd+s+ m +qel+t+++y +p+k+v+lnn ++Gmv+qWqe
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 429 GGLGTMGYGLPAAIGAQLAHPEAQVACISGDASILMCIQELATCQQYRLPIKVVLLNNGYMGMVRQWQE 497
                                               ********************************************************************* PP

                                 TIGR00118 476 lfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPm 543
                                               lfye rys++++ + lpdfvklae++G++g+r+e+pe le++++ea++++ + v+ldv vd +e+v+Pm
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 498 LFYESRYSHSYVDA-LPDFVKLAESFGHVGMRVERPEHLEDAMREAFAMRdRFVFLDVIVDPTENVYPM 565
                                               *************5.*******************************9987689**************** PP

                                 TIGR00118 544 vapGagldelv 554
                                               +a G+g +e+ 
  lcl|NCBI__GCF_000025485.1:WP_012970167.1 566 IAAGKGHHEMQ 576
                                               *********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (587 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: 11.69
//
[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