Alignments for a candidate for ilvI in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Crocosphaera subtropica ATCC 51142

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_009543467.1 CCE_RS21080 biosynthetic-type acetolactate synthase large subunit

Query= BRENDA::P9WG41
         (618 letters)



>NCBI__GCF_000017845.1:WP_009543467.1
          Length = 619

 Score =  554 bits (1427), Expect = e-162
 Identities = 297/571 (52%), Positives = 381/571 (66%), Gaps = 13/571 (2%)

Query: 36  QQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKK---LRHVLVRHEQGAGHAA 92
           Q+ TGA A+I SL   GV  IFG PGGA+LP+YD L+ ++    ++H LVRHEQGA HAA
Sbjct: 17  QRRTGAYALIDSLVRHGVKHIFGYPGGAILPIYDELYRAEARGDIQHFLVRHEQGASHAA 76

Query: 93  SGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADI 152
            GYA  TG+VGVC  TSGPGATNLVT +A A +DSIP+V +TGQVGR  IG+DAFQE DI
Sbjct: 77  DGYARATGKVGVCFGTSGPGATNLVTGIATAHLDSIPMVVVTGQVGRAAIGSDAFQETDI 136

Query: 153 SGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTF--SWPP 210
            GIT+PI KH+++VR  +D+ +++AEAFHIA++GRPG VL+D+PKDV   +C +    P 
Sbjct: 137 FGITLPIVKHSYVVRHAEDMAKIVAEAFHIASTGRPGPVLIDVPKDVGLEECDYIPVEPG 196

Query: 211 RMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVV 270
           +++LPGY+P  K + RQ+  A  LI  + +P+LYVGGG I   A  Q++ELAE   IPV 
Sbjct: 197 QVKLPGYRPTVKGNPRQINAALSLIETSERPLLYVGGGAIAANAHAQVQELAERFQIPVT 256

Query: 271 TTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFAPEA 330
           TTLM  G+F + H  ++GM GMHGT  A  A+   DLLIA+G RFDDRVTGKLD FA  A
Sbjct: 257 TTLMGIGSFDEHHPLSVGMLGMHGTAYANFAVSECDLLIAVGARFDDRVTGKLDEFASRA 316

Query: 331 KVIHADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIE-MADWWAYLNGVR 389
           +VIH DIDPAE+GKNR  +VPIVGDV+ V+ +L+   R   +P   E    W   +N  R
Sbjct: 317 RVIHIDIDPAEVGKNRLPEVPIVGDVRQVLEQLLQRSREIDVPLDAEKTTPWLNRINRWR 376

Query: 390 KTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPRSWLNS 449
           + YPL   P  D  +SP+ VI ++G  A P A +   VGQHQMWAAQF+    PR W++S
Sbjct: 377 EQYPL-VAPHYDHRISPQEVIVEVGRQA-PHAYYTTDVGQHQMWAAQFLN-NGPRRWISS 433

Query: 450 GGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINNGN 509
            GLGTMG+ +PAAMG K+ALP  EV  I GD  FQM  QELAT A   I  K  +INNG 
Sbjct: 434 AGLGTMGYGMPAAMGVKVALPEEEVICISGDASFQMNLQELATLAQYNIAAKTVIINNGW 493

Query: 510 LGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVINQARA 569
            GMVRQWQ  FY ERYS +++ T    +PDF  LA+A G  G+       +   + +  A
Sbjct: 494 QGMVRQWQQTFYGERYSSSNMQT---GMPDFELLAKAFGVKGITVTEHSQLAGAVAEMLA 550

Query: 570 INDCPVVIDFIVGADAQVWPMVAAGTSNDEI 600
            +D PV++D  V  D   +PMVA G SN ++
Sbjct: 551 -HDGPVLMDVHVKRDENCYPMVAPGKSNAQM 580


Lambda     K      H
   0.319    0.136    0.414 

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: 1171
Number of extensions: 61
Number of successful extensions: 6
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: 618
Length of database: 619
Length adjustment: 37
Effective length of query: 581
Effective length of database: 582
Effective search space:   338142
Effective search space used:   338142
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_009543467.1 CCE_RS21080 (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.3916548.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-269  881.0   0.2   1.8e-269  880.8   0.2    1.0  1  NCBI__GCF_000017845.1:WP_009543467.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017845.1:WP_009543467.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  880.8   0.2  1.8e-269  1.8e-269       2     555 ..      20     582 ..      19     584 .. 0.98

  Alignments for each domain:
  == domain 1  score: 880.8 bits;  conditional E-value: 1.8e-269
                             TIGR00118   2 kgaeilveslkkegvetvfGyPGGavlpiydaly....dselehilvrheqaaahaadGyarasGkvGvvlat 70 
                                           +ga++l++sl ++gv+++fGyPGGa+lpiyd+ly     ++++h lvrheq+a+haadGyara+GkvGv+++t
  NCBI__GCF_000017845.1:WP_009543467.1  20 TGAYALIDSLVRHGVKHIFGYPGGAILPIYDELYraeaRGDIQHFLVRHEQGASHAADGYARATGKVGVCFGT 92 
                                           79********************************9888899******************************** PP

                             TIGR00118  71 sGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafe 143
                                           sGPGatnlvtgiata+lds+P+vv+tGqv +++iGsdafqe di+Gitlp++khs++v++aed+++i+ eaf+
  NCBI__GCF_000017845.1:WP_009543467.1  93 SGPGATNLVTGIATAHLDSIPMVVVTGQVGRAAIGSDAFQETDIFGITLPIVKHSYVVRHAEDMAKIVAEAFH 165
                                           ************************************************************************* PP

                             TIGR00118 144 iastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviia 214
                                           iastGrPGPvl+d+Pkdv  +e+++      +v+lpgy+ptvkg+++qi++al lie++++P+l+vGgG+i+a
  NCBI__GCF_000017845.1:WP_009543467.1 166 IASTGRPGPVLIDVPKDVGLEECDYIPVepGQVKLPGYRPTVKGNPRQINAALSLIETSERPLLYVGGGAIAA 238
                                           ************************9877679****************************************** PP

                             TIGR00118 215 easeelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlak 287
                                           +a+++++elaer++ipvtttl+G+G+f+e+hpl++gmlGmhGt++an+avse+dlliavGarfddrvtg+l++
  NCBI__GCF_000017845.1:WP_009543467.1 239 NAHAQVQELAERFQIPVTTTLMGIGSFDEHHPLSVGMLGMHGTAYANFAVSECDLLIAVGARFDDRVTGKLDE 311
                                           ************************************************************************* PP

                             TIGR00118 288 fapeakiihididPaeigknvkvdipivGdakkvleellkklkee.....ekkekeWlekieewkkeyilkld 355
                                           fa++a++ihididPae+gkn+  ++pivGd+++vle+ll++ +e       +k++ Wl++i++w+++y+l   
  NCBI__GCF_000017845.1:WP_009543467.1 312 FASRARVIHIDIDPAEVGKNRLPEVPIVGDVRQVLEQLLQRSREIdvpldAEKTTPWLNRINRWREQYPLVAP 384
                                           *****************************************999888885444545***************** PP

                             TIGR00118 356 eeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpe 428
                                           ++++ i Pq+vi e+ ++++ +a++ttdvGqhqmwaaqf+++  pr++i+s+GlGtmG+G+Paa+G+kva pe
  NCBI__GCF_000017845.1:WP_009543467.1 385 HYDHRISPQEVIVEVGRQAP-HAYYTTDVGQHQMWAAQFLNNG-PRRWISSAGLGTMGYGMPAAMGVKVALPE 455
                                           *******************9.7******************998.***************************** PP

                             TIGR00118 429 etvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeay 501
                                           e+v++++Gd+sfqmnlqel+t+++y+i  k+vi+nn ++Gmv+qWq++fy erys++++++++pdf+ la+a+
  NCBI__GCF_000017845.1:WP_009543467.1 456 EEVICISGDASFQMNLQELATLAQYNIAAKTVIINNGWQGMVRQWQQTFYGERYSSSNMQTGMPDFELLAKAF 528
                                           ************************************************************************* PP

                             TIGR00118 502 GvkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555
                                           Gvkgi+++++++l+ +++e+l++++pvl+dv+v+++e+++PmvapG++++++++
  NCBI__GCF_000017845.1:WP_009543467.1 529 GVKGITVTEHSQLAGAVAEMLAHDGPVLMDVHVKRDENCYPMVAPGKSNAQMIG 582
                                           ****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (619 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: 00:00:00.01
# Mc/sec: 17.46
//
[ok]

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

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

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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