Alignments for a candidate for ilvI in Acidithiobacillus ferrooxidans ATCC 23270

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Acidithiobacillus ferrooxidans ATCC 23270

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012536327.1 AFE_RS03530 biosynthetic-type acetolactate synthase large subunit

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



>NCBI__GCF_000021485.1:WP_012536327.1
          Length = 581

 Score =  798 bits (2061), Expect = 0.0
 Identities = 379/563 (67%), Positives = 461/563 (81%), Gaps = 1/563 (0%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           E+ GAEI+V AL +EGVEYV+GYPGGAVLYIYD+L ++   +HILVRHEQAAVHAAD Y+
Sbjct: 19  ELTGAEIVVRALRDEGVEYVFGYPGGAVLYIYDKLAQEDAVKHILVRHEQAAVHAADAYS 78

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R TGKVGV LVTSGPG TNAVTGIATAY+DS+P+VVITG VP   IG DAFQE DTVGIT
Sbjct: 79  RVTGKVGVVLVTSGPGATNAVTGIATAYMDSVPLVVITGQVPVALIGNDAFQEVDTVGIT 138

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHNFLVKDVRDLA+T+K AF++AATGRPGPV+VDIPKD++ +   Y YP+ I +RS
Sbjct: 139 RPCTKHNFLVKDVRDLASTLKTAFYLAATGRPGPVLVDIPKDITSHKAAYHYPEKITLRS 198

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257
           Y P  KGHSGQ+RKA+ ++ GA+RP  YTGGG++L NAS+ LR+L    G P+T+TLMGL
Sbjct: 199 YKPTVKGHSGQVRKAMQIITGAQRPMFYTGGGIILGNASEALRKLVRTLGVPITHTLMGL 258

Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317
           GA+P + +QF+GMLGMHGTYEANMA+Q+CDVL+A+GARFDDRV GN A F   AR I+H+
Sbjct: 259 GAYPASDRQFLGMLGMHGTYEANMAVQHCDVLVALGARFDDRVTGNLAKFAPHAR-IVHV 317

Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377
           D+DPSSISK V+VD+P+VG+++ VL E+   ++ +D +   +A+  WW QIE+WR  DCL
Sbjct: 318 DVDPSSISKNVRVDVPVVGDLQQVLLEMNHMLEENDQRNDPQAMQTWWAQIEEWRGRDCL 377

Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437
            Y++   +IKPQ+VV+K++ELT+G+A I SDVGQHQMWAAQFY FD PRRW+NSGGLGTM
Sbjct: 378 HYNQDDRVIKPQFVVQKLFELTEGNAIITSDVGQHQMWAAQFYGFDRPRRWVNSGGLGTM 437

Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497
           G GLP AMG + A P+  VV ITG+GSIQM IQELSTCLQY  PVK+  LNN YLGMVRQ
Sbjct: 438 GFGLPAAMGAQVAEPDSTVVCITGDGSIQMNIQELSTCLQYRLPVKVACLNNHYLGMVRQ 497

Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557
           WQE  Y+NRY+ SY+DALPDFVKLAEAYGHVG+R    +DVEP +REA RLKDR VF+DF
Sbjct: 498 WQEFFYENRYAMSYVDALPDFVKLAEAYGHVGLRAHTPADVEPVIREALRLKDRMVFMDF 557

Query: 558 QTDPTENVWPMVQAGKGISEMLL 580
           Q DPTENV+PMV AG  +SEM+L
Sbjct: 558 QVDPTENVYPMVPAGAALSEMIL 580


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: 1052
Number of extensions: 40
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: 581
Length adjustment: 36
Effective length of query: 549
Effective length of database: 545
Effective search space:   299205
Effective search space used:   299205
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_012536327.1 AFE_RS03530 (biosynthetic-type acetolactate synthase large subunit)
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.4159042.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-266  869.9   0.9     4e-266  869.7   0.9    1.0  1  NCBI__GCF_000021485.1:WP_012536327.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021485.1:WP_012536327.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  869.7   0.9    4e-266    4e-266       1     555 [.      20     580 ..      20     581 .] 0.98

  Alignments for each domain:
  == domain 1  score: 869.7 bits;  conditional E-value: 4e-266
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                           l+gaei+v++l++egve+vfGyPGGavl iyd+l  ++ ++hilvrheqaa+haad y+r++GkvGvvl+tsG
  NCBI__GCF_000021485.1:WP_012536327.1  20 LTGAEIVVRALRDEGVEYVFGYPGGAVLYIYDKLAqEDAVKHILVRHEQAAVHAADAYSRVTGKVGVVLVTSG 92 
                                           68********************************98899********************************** PP

                             TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145
                                           PGatn+vtgiatay+dsvPlvv+tGqv+ +liG+dafqe+d +Git+p+tkh+flvk+++dl+++lk af++a
  NCBI__GCF_000021485.1:WP_012536327.1  93 PGATNAVTGIATAYMDSVPLVVITGQVPVALIGNDAFQEVDTVGITRPCTKHNFLVKDVRDLASTLKTAFYLA 165
                                           ************************************************************************* PP

                             TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218
                                           +tGrPGPvlvd+Pkd+t+++  ++++ek++l++ykptvkgh  q++ka+++i+ a++P+ + GgG+i ++ase
  NCBI__GCF_000021485.1:WP_012536327.1 166 ATGRPGPVLVDIPKDITSHKAAYHYPEKITLRSYKPTVKGHSGQVRKAMQIITGAQRPMFYTGGGIILGNASE 238
                                           ************************************************************************* PP

                             TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291
                                            l++l+ +l +p+t+tl+GlGa+p+ ++++lgmlGmhGt+ean+av+++d+l+a+Garfddrvtgnlakfap+
  NCBI__GCF_000021485.1:WP_012536327.1 239 ALRKLVRTLGVPITHTLMGLGAYPASDRQFLGMLGMHGTYEANMAVQHCDVLVALGARFDDRVTGNLAKFAPH 311
                                           ************************************************************************* PP

                             TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilkldeeee 359
                                           a+i+h+d+dP++i+knv+vd+p+vGd ++vl e+ + l+e+    + + ++ W+++ieew+ + +l++++++ 
  NCBI__GCF_000021485.1:WP_012536327.1 312 ARIVHVDVDPSSISKNVRVDVPVVGDLQQVLLEMNHMLEENdqrnDPQAMQtWWAQIEEWRGRDCLHYNQDDR 384
                                           ********************************99999888865553444567********************* PP

                             TIGR00118 360 sikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvv 432
                                            ikPq v+++l +l++++ai+t+dvGqhqmwaaqfy +++pr++++sgGlGtmGfGlPaa+Ga+va+p++tvv
  NCBI__GCF_000021485.1:WP_012536327.1 385 VIKPQFVVQKLFELTEGNAIITSDVGQHQMWAAQFYGFDRPRRWVNSGGLGTMGFGLPAAMGAQVAEPDSTVV 457
                                           ************************************************************************* PP

                             TIGR00118 433 avtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkg 505
                                           ++tGdgs+qmn+qelst+ +y +pvk+ +lnn++lGmv+qWqe+fye+ry+ +++ + lpdfvklaeayG++g
  NCBI__GCF_000021485.1:WP_012536327.1 458 CITGDGSIQMNIQELSTCLQYRLPVKVACLNNHYLGMVRQWQEFFYENRYAMSYVDA-LPDFVKLAEAYGHVG 529
                                           ********************************************************5.*************** PP

                             TIGR00118 506 iriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelve 555
                                           +r ++p+++e  ++eal+ k ++v++d++vd +e+v+Pmv+ Ga+l+e++ 
  NCBI__GCF_000021485.1:WP_012536327.1 530 LRAHTPADVEPVIREALRLKdRMVFMDFQVDPTENVYPMVPAGAALSEMIL 580
                                           *****************988689**************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (581 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 34.51
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Protein sequences (fasta format)
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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