Alignments for a candidate for ilvI in Thioalkalivibrio paradoxus ARh 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Thioalkalivibrio paradoxus ARh 1

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_006745875.1 THITH_RS03515 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000227685.2:WP_006745875.1
          Length = 572

 Score =  799 bits (2063), Expect = 0.0
 Identities = 388/571 (67%), Positives = 459/571 (80%), Gaps = 2/571 (0%)

Query: 11  SNSSAAPEMI-GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAA 69
           S +SA P  I GAEI V  L EEGVE V+GYPGGAVL+IYD L++Q K  HILVRHEQ A
Sbjct: 2   SETSAKPTAITGAEIFVRCLQEEGVEVVFGYPGGAVLHIYDALYRQDKVSHILVRHEQGA 61

Query: 70  VHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQ 129
           VHAA+GYA+++ + GVALVTSGPG TNAVTGIA AY+DS+P+VV TG VPT+ IG DAFQ
Sbjct: 62  VHAAEGYAKSSNQCGVALVTSGPGATNAVTGIADAYMDSVPLVVFTGQVPTNLIGNDAFQ 121

Query: 130 ECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEY 189
           E DTVGITRP VKHNFLVKDV DLA TIKKAF++A TGRPGPVVVDIPKDV+     +EY
Sbjct: 122 EVDTVGITRPCVKHNFLVKDVNDLATTIKKAFYVATTGRPGPVVVDIPKDVTAQTAVFEY 181

Query: 190 PKSIDMRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHP 249
           PK I MRSYNP  +GH GQIRKA+ L+  A++P +YTGGG++L  AS+ L +     G+P
Sbjct: 182 PKQIRMRSYNPTTRGHGGQIRKALDLILSAQKPMLYTGGGIILGQASEALTEFTRRLGYP 241

Query: 250 VTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTS 309
           +TNTLMGLG FP +   F+GMLGMHGTYEANMAM   DV+IAIGARFDDRV GN   F  
Sbjct: 242 ITNTLMGLGGFPASDPLFLGMLGMHGTYEANMAMHYADVVIAIGARFDDRVTGNIEKFCP 301

Query: 310 QARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIE 369
            A KI+HID+DP+SISK VKVD+PIVG V+ VL+E++ ++++ + +P  EALA WW QIE
Sbjct: 302 YA-KIVHIDVDPASISKNVKVDVPIVGQVEPVLREMLRELESMNREPDAEALAAWWRQIE 360

Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWI 429
           +WR+ DCLK+DR+S IIKPQ VV+K+WELT GDA + SDVGQHQMWAAQFY+FD+P RWI
Sbjct: 361 EWRAKDCLKFDRASPIIKPQLVVQKLWELTGGDAIVTSDVGQHQMWAAQFYRFDKPNRWI 420

Query: 430 NSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNN 489
           NSGGLGTMGVGLP+AMG + A P+  V  ITGE SIQMCIQELSTCLQY  P+KI +LNN
Sbjct: 421 NSGGLGTMGVGLPFAMGAQFANPDATVACITGEASIQMCIQELSTCLQYQLPIKIVNLNN 480

Query: 490 GYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLK 549
            YLGMVRQWQE  Y  RY+ SYMDALPDFVKLAE+YGHVGMR+E+  DVE ALREA  +K
Sbjct: 481 RYLGMVRQWQEFFYQGRYAMSYMDALPDFVKLAESYGHVGMRIEQPGDVEGALREALAMK 540

Query: 550 DRTVFLDFQTDPTENVWPMVQAGKGISEMLL 580
           DR VFLDF TD +ENV+PM+ AG G +EM+L
Sbjct: 541 DRLVFLDFITDQSENVYPMIPAGAGQNEMIL 571


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: 1029
Number of extensions: 35
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: 572
Length adjustment: 36
Effective length of query: 549
Effective length of database: 536
Effective search space:   294264
Effective search space used:   294264
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_006745875.1 THITH_RS03515 (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.11765.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-264  863.0   0.2   4.9e-264  862.8   0.2    1.0  1  lcl|NCBI__GCF_000227685.2:WP_006745875.1  THITH_RS03515 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006745875.1  THITH_RS03515 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  862.8   0.2  4.9e-264  4.9e-264       2     555 ..      12     571 ..      11     572 .] 0.98

  Alignments for each domain:
  == domain 1  score: 862.8 bits;  conditional E-value: 4.9e-264
                                 TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvla 69 
                                               +gaei+v+ l++egve+vfGyPGGavl+iydaly +++++hilvrheq+a+haa+Gya++s + Gv+l+
  lcl|NCBI__GCF_000227685.2:WP_006745875.1  12 TGAEIFVRCLQEEGVEVVFGYPGGAVLHIYDALYrQDKVSHILVRHEQGAVHAAEGYAKSSNQCGVALV 80 
                                               89********************************99********************************* PP

                                 TIGR00118  70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138
                                               tsGPGatn+vtgia+ay+dsvPlvv+tGqv+t+liG+dafqe+d +Git+p++kh+flvk+++dl++++
  lcl|NCBI__GCF_000227685.2:WP_006745875.1  81 TSGPGATNAVTGIADAYMDSVPLVVFTGQVPTNLIGNDAFQEVDTVGITRPCVKHNFLVKDVNDLATTI 149
                                               ********************************************************************* PP

                                 TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllv 207
                                               k+af++a+tGrPGPv+vd+Pkdvt+++  +e+++++ +++y+pt++gh  qi+kal+li +a+kP+l+ 
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 150 KKAFYVATTGRPGPVVVDIPKDVTAQTAVFEYPKQIRMRSYNPTTRGHGGQIRKALDLILSAQKPMLYT 218
                                               ********************************************************************* PP

                                 TIGR00118 208 GgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGar 276
                                               GgG+i ++ase l+e++ rl  p+t tl+GlG+fp+ +pl+lgmlGmhGt+ean+a++ ad++ia+Gar
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 219 GGGIILGQASEALTEFTRRLGYPITNTLMGLGGFPASDPLFLGMLGMHGTYEANMAMHYADVVIAIGAR 287
                                               ********************************************************************* PP

                                 TIGR00118 277 fddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wl 340
                                               fddrvtgn++kf+p aki+hid+dPa+i+knvkvd+pivG+++ vl+e+l++l+++    + +    W+
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 288 FDDRVTGNIEKFCPYAKIVHIDVDPASISKNVKVDVPIVGQVEPVLREMLRELESMnrepDAEALAaWW 356
                                               ***************************************************9998866543333347** PP

                                 TIGR00118 341 ekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGl 409
                                               ++ieew+++ +lk+d+ +  ikPq v+++l++l+ ++aivt+dvGqhqmwaaqfy+++kp+++i+sgGl
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 357 RQIEEWRAKDCLKFDRASPIIKPQLVVQKLWELTGGDAIVTSDVGQHQMWAAQFYRFDKPNRWINSGGL 425
                                               ********************************************************************* PP

                                 TIGR00118 410 GtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfy 478
                                               GtmG GlP a+Ga+ a+p++tv ++tG++s+qm +qelst+ +y++p+kiv+lnn++lGmv+qWqe+fy
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 426 GTMGVGLPFAMGAQFANPDATVACITGEASIQMCIQELSTCLQYQLPIKIVNLNNRYLGMVRQWQEFFY 494
                                               ********************************************************************* PP

                                 TIGR00118 479 eerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvap 546
                                               ++ry+ +++ + lpdfvklae+yG++g+rie+p ++e +l+eal++k ++v+ld+  d++e+v+Pm++ 
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 495 QGRYAMSYMDA-LPDFVKLAESYGHVGMRIEQPGDVEGALREALAMKdRLVFLDFITDQSENVYPMIPA 562
                                               **********5.********************************988799******************* PP

                                 TIGR00118 547 Gagldelve 555
                                               Gag +e++ 
  lcl|NCBI__GCF_000227685.2:WP_006745875.1 563 GAGQNEMIL 571
                                               *******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (572 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 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.57
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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