Alignments for a candidate for ilvI in Azoarcus sp. BH72

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Azoarcus sp. BH72

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011766879.1 AZO_RS15825 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_000061505.1:WP_011766879.1
          Length = 570

 Score =  838 bits (2164), Expect = 0.0
 Identities = 402/568 (70%), Positives = 478/568 (84%), Gaps = 1/568 (0%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYAR 78
           + GAEI++  L EE VEYV+GYPGGAVLYIYD L +Q +  H+LVRHEQAAVHAADG+AR
Sbjct: 3   LTGAEIVIRCLQEEKVEYVFGYPGGAVLYIYDALFQQEQVRHVLVRHEQAAVHAADGFAR 62

Query: 79  ATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITR 138
           +T KVGVALVTSGPG TNAVTGIATA+ DSIPMV+I+G VPT AIGQDAFQE DTVGITR
Sbjct: 63  STEKVGVALVTSGPGATNAVTGIATAFCDSIPMVIISGQVPTAAIGQDAFQEVDTVGITR 122

Query: 139 PIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSY 198
           P VKHNFLVKDVRD+AATIKKAF++A TGRPGPV+VDIPKD++   C +EYPK I MRSY
Sbjct: 123 PCVKHNFLVKDVRDIAATIKKAFYLAKTGRPGPVLVDIPKDITIAKCDFEYPKEISMRSY 182

Query: 199 NPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLG 258
           +PV KGH GQI+KAV LL  A+RP IYTGGGVVLANA+++L +L  L G PVTNTLMGLG
Sbjct: 183 SPVVKGHQGQIKKAVQLLLEAKRPMIYTGGGVVLANAAEQLTKLTRLLGFPVTNTLMGLG 242

Query: 259 AFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHID 318
            +P + +Q++GM GMHGTYEANMAM   DVL+A+GARFDDRVIGNPA+F  + RKIIHID
Sbjct: 243 GYPASDRQYLGMPGMHGTYEANMAMHYSDVLLAVGARFDDRVIGNPANFAEEPRKIIHID 302

Query: 319 IDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLK 378
           IDPSSISKRVKVD+PIVG++KDVL E+I Q++A+  +P    LA WW+Q+E+WRS  C++
Sbjct: 303 IDPSSISKRVKVDVPIVGDLKDVLDEMIRQLEAAPTRPDASNLAAWWKQVEEWRSRKCME 362

Query: 379 YDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMG 438
           Y  S EIIKPQ+VV+K+WE+T GDA + SDVGQHQMWA+Q+Y+FD+PRRW+NSGGLGTMG
Sbjct: 363 YKNSDEIIKPQFVVQKLWEVTGGDAIVTSDVGQHQMWASQYYRFDKPRRWLNSGGLGTMG 422

Query: 439 VGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQW 498
           VGLPYAMG + A P+  V  +TGE SIQMCIQELSTC Q+  P+KIC+LNN YLGMVRQW
Sbjct: 423 VGLPYAMGAQFAHPDMPVACVTGEASIQMCIQELSTCKQFRLPIKICNLNNRYLGMVRQW 482

Query: 499 QEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL-KDRTVFLDF 557
           Q++ +  RYS SYMD+LPDF KLA AYGHVG+RV+K +DVE ALREAF   K+  VFLDF
Sbjct: 483 QQLFHGGRYSESYMDSLPDFAKLASAYGHVGIRVDKPADVEGALREAFTTHKNDLVFLDF 542

Query: 558 QTDPTENVWPMVQAGKGISEMLLGAEDL 585
           Q DPTENV+PMVQ GKG++EM+L AEDL
Sbjct: 543 QVDPTENVYPMVQGGKGLTEMILSAEDL 570


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: 1073
Number of extensions: 34
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: 570
Length adjustment: 36
Effective length of query: 549
Effective length of database: 534
Effective search space:   293166
Effective search space used:   293166
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_011766879.1 AZO_RS15825 (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.19689.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-256  836.3   0.1   6.5e-256  836.0   0.1    1.0  1  lcl|NCBI__GCF_000061505.1:WP_011766879.1  AZO_RS15825 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011766879.1  AZO_RS15825 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  836.0   0.1  6.5e-256  6.5e-256       1     555 [.       3     565 ..       3     567 .. 0.98

  Alignments for each domain:
  == domain 1  score: 836.0 bits;  conditional E-value: 6.5e-256
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei+++ l++e+ve+vfGyPGGavl iydal+ +++++h+lvrheqaa+haadG+ar++ kvGv+l
  lcl|NCBI__GCF_000061505.1:WP_011766879.1   3 LTGAEIVIRCLQEEKVEYVFGYPGGAVLYIYDALFqQEQVRHVLVRHEQAAVHAADGFARSTEKVGVAL 71 
                                               68*********************************8899****************************** PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtgiata+ ds+P+v+++Gqv+t++iG+dafqe+d +Git+p++kh+flvk+++d++++
  lcl|NCBI__GCF_000061505.1:WP_011766879.1  72 VTSGPGATNAVTGIATAFCDSIPMVIISGQVPTAAIGQDAFQEVDTVGITRPCVKHNFLVKDVRDIAAT 140
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               +k+af++a+tGrPGPvlvd+Pkd+t a++++e+++++++++y p vkgh+ qikka++l+ +ak+P+++
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 141 IKKAFYLAKTGRPGPVLVDIPKDITIAKCDFEYPKEISMRSYSPVVKGHQGQIKKAVQLLLEAKRPMIY 209
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275
                                                GgGv+ a+a e+l++l+  l  pvt tl+GlG++p+ +++ lgm GmhGt+ean+a++ +d+l+avGa
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 210 TGGGVVLANAAEQLTKLTRLLGFPVTNTLMGLGGYPASDRQYLGMPGMHGTYEANMAMHYSDVLLAVGA 278
                                               ********************************************************************* PP

                                 TIGR00118 276 rfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338
                                               rfddrv gn a+fa+e  kiihididP++i+k vkvd+pivGd k vl+e++++l++     + ++   
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 279 RFDDRVIGNPANFAEEPrKIIHIDIDPSSISKRVKVDVPIVGDLKDVLDEMIRQLEAAptrpDASNLAa 347
                                               **************99626************************************99987765556557 PP

                                 TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407
                                               W++++eew++++++++++++e ikPq v+++l++++ ++aivt+dvGqhqmwa+q+y+++kpr++++sg
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 348 WWKQVEEWRSRKCMEYKNSDEIIKPQFVVQKLWEVTGGDAIVTSDVGQHQMWASQYYRFDKPRRWLNSG 416
                                               ********************************************************************* PP

                                 TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476
                                               GlGtmG GlP a+Ga+ a+p+  v +vtG++s+qm +qelst++++ +p+ki++lnn++lGmv+qWq+l
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 417 GLGTMGVGLPYAMGAQFAHPDMPVACVTGEASIQMCIQELSTCKQFRLPIKICNLNNRYLGMVRQWQQL 485
                                               ********************************************************************* PP

                                 TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPm 543
                                               f+ +ryse+++ s lpdf+kla ayG++gir+ kp+++e +l+ea++++  ++v+ld++vd +e+v+Pm
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 486 FHGGRYSESYMDS-LPDFAKLASAYGHVGIRVDKPADVEGALREAFTTHknDLVFLDFQVDPTENVYPM 553
                                               ************5.*******************************98764589**************** PP

                                 TIGR00118 544 vapGagldelve 555
                                               v  G+gl+e++ 
  lcl|NCBI__GCF_000061505.1:WP_011766879.1 554 VQGGKGLTEMIL 565
                                               **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (570 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: 00:00:00.03
# Mc/sec: 8.49
//
[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