Alignments for a candidate for ilvI in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Steroidobacter denitrificans DSM 18526

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_083537097.1 ACG33_RS00740 acetolactate synthase, large subunit, biosynthetic type

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



>NCBI__GCF_001579945.1:WP_083537097.1
          Length = 596

 Score =  429 bits (1104), Expect = e-124
 Identities = 254/580 (43%), Positives = 337/580 (58%), Gaps = 21/580 (3%)

Query: 19  MIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELH---------KQTKFEHILVRHEQAA 69
           M GAEI+V  LA+EGV+ V+GY GGA+L  YD +           + +   I+  +EQ A
Sbjct: 1   MTGAEIIVQVLADEGVDTVFGYSGGAILPTYDAIFVNNQDCERCDRRQMSLIVPANEQGA 60

Query: 70  VHAADGYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQ 129
              A GYARATGKVGV +VTSGPG TN VT +     DSIP+VVI G VPT AIG DAFQ
Sbjct: 61  GFMAAGYARATGKVGVCIVTSGPGATNTVTPVRDCMADSIPIVVICGQVPTGAIGSDAFQ 120

Query: 130 ECDTVGITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEY 189
           E     I   + KH FLV D   L ATI+ AF IA +GRPGPVV+D+PKDV     K++ 
Sbjct: 121 EAPVASIMGAVAKHVFLVTDPSKLEATIRTAFEIARSGRPGPVVIDVPKDVQNWQGKFQG 180

Query: 190 PKSIDMRSYNP--VNKGHS----GQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLA 243
              + +  Y        HS     +  +   +L  A RP IY GGGV+ +  S  L++ A
Sbjct: 181 AGRLPVAGYRQRMTRLTHSVLSDARCAEFFTMLGAARRPLIYAGGGVIHSGGSQALQEFA 240

Query: 244 ALTGHPVTNTLMGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGN 303
              G PV  TLMGLGA   T    + MLGMHG   AN A+ +CD L A+GARFDDRV GN
Sbjct: 241 IEYGIPVVTTLMGLGALDTTHPLAMRMLGMHGAAFANYAVDDCDFLFALGARFDDRVAGN 300

Query: 304 PAHFTSQARKIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAK 363
           PA F   A++I  IDID S I+K  +V    +G + + L+ LI   + S         + 
Sbjct: 301 PAKFAPNAKQIAQIDIDISEINKVKQVHWHHIGLLPEALRGLIDYGRRSAFN---RDWST 357

Query: 364 WWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFD 423
           W    +Q R    + Y+R SE I+P +V+E+I +LT+G+A I + VGQHQMWAAQ++ F 
Sbjct: 358 WRTHCDQLRRTYAMNYERDSERIQPYHVIEEINKLTRGEAIITTGVGQHQMWAAQYFDFR 417

Query: 424 EPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVK 483
            PR W+ SG +GTMG GLP A+G + A P++ V+ I G+ SI+M + EL T   Y  P+K
Sbjct: 418 SPRLWLTSGSMGTMGFGLPAAIGAQFAQPDRLVIDIDGDSSIRMNLGELETVTTYGLPIK 477

Query: 484 ICSLNNGYLGMVRQWQEIEYDNRYSHSYMDA-LPDFVKLAEAYGH-VGMRVEKTSDVEPA 541
           +  LNN   GMV+QWQ++ +  R + S       DF+K AEA G    MR+E+  DV   
Sbjct: 478 VVVLNNCGDGMVKQWQKLFFKGRLAASDRSLHKKDFLKAAEADGFPYVMRLERPQDVARV 537

Query: 542 LREAFRLKDRTVFLDFQTDPTENVWPMVQAGKGISEMLLG 581
           ++E    +    FL+   DP   V+PMV  G+  SEM+ G
Sbjct: 538 VKEFVEFQG-PAFLEVMIDPDAGVYPMVGPGQPYSEMITG 576


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: 896
Number of extensions: 51
Number of successful extensions: 5
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: 596
Length adjustment: 37
Effective length of query: 548
Effective length of database: 559
Effective search space:   306332
Effective search space used:   306332
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_083537097.1 ACG33_RS00740 (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.30156.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-199  650.4   0.0   1.3e-199  650.2   0.0    1.0  1  lcl|NCBI__GCF_001579945.1:WP_083537097.1  ACG33_RS00740 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_083537097.1  ACG33_RS00740 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  650.2   0.0  1.3e-199  1.3e-199       1     555 [.       1     575 [.       1     577 [. 0.95

  Alignments for each domain:
  == domain 1  score: 650.2 bits;  conditional E-value: 1.3e-199
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..........dselehilvrheqaaahaadGyar 59 
                                               ++gaei+v+ l +egv+tvfGy GGa+lp yda++            +++ i++  eq+a  +a Gyar
  lcl|NCBI__GCF_001579945.1:WP_083537097.1   1 MTGAEIIVQVLADEGVDTVFGYSGGAILPTYDAIFvnnqdcercdRRQMSLIVPANEQGAGFMAAGYAR 69 
                                               79*********************************8765444433346899****************** PP

                                 TIGR00118  60 asGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflv 128
                                               a+GkvGv+++tsGPGatn+vt++ + ++ds+P+vv+ Gqv+t +iGsdafqe+ +  i+ +v kh flv
  lcl|NCBI__GCF_001579945.1:WP_083537097.1  70 ATGKVGVCIVTSGPGATNTVTPVRDCMADSIPIVVICGQVPTGAIGSDAFQEAPVASIMGAVAKHVFLV 138
                                               ********************************************************************* PP

                                 TIGR00118 129 kkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklq......ik 191
                                               ++++ l ++++ afeia +GrPGPv++d+Pkdv++ + +++   ++ + gy+ +++  ++        +
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 139 TDPSKLEATIRTAFEIARSGRPGPVVIDVPKDVQNWQGKFQGAGRLPVAGYRQRMTRLTHSvlsdarCA 207
                                               ***************************************************987664443322333366 PP

                                 TIGR00118 192 kaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkea 260
                                               +   ++ +a++P++++GgGvi++++s+ l+e+a +  ipv+ttl+GlGa++ +hpla+ mlGmhG++ a
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 208 EFFTMLGAARRPLIYAGGGVIHSGGSQALQEFAIEYGIPVVTTLMGLGALDTTHPLAMRMLGMHGAAFA 276
                                               6678899************************************************************** PP

                                 TIGR00118 261 nlavseadlliavGarfddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkk 328
                                               n+av+++d l+a+Garfddrv+gn akfap+ak i  idid +ei+k+ +v+   +G   + l+ l++ 
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 277 NYAVDDCDFLFALGARFDDRVAGNPAKFAPNAKqIAQIDIDISEINKVKQVHWHHIGLLPEALRGLIDY 345
                                               ********************************97889******************************98 PP

                                 TIGR00118 329 lkee..ekkekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfy 395
                                                ++   +++ + W  + ++++++y +++++++e i+P +vi+e+ kl+++eai+tt+vGqhqmwaaq++
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 346 GRRSafNRDWSTWRTHCDQLRRTYAMNYERDSERIQPYHVIEEINKLTRGEAIITTGVGQHQMWAAQYF 414
                                               887764555556********************************************************* PP

                                 TIGR00118 396 ktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnn 464
                                               ++++pr ++tsg +GtmGfGlPaa+Ga+ a+p+  v++++Gd+s+ mnl el+t++ y++p+k+v+lnn
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 415 DFRSPRLWLTSGSMGTMGFGLPAAIGAQFAQPDRLVIDIDGDSSIRMNLGELETVTTYGLPIKVVVLNN 483
                                               ********************************************************************* PP

                                 TIGR00118 465 ellGmvkqWqelfyeerysetklaselpdfvklaeayGv.kgiriekpeeleeklkealeskepvlldv 532
                                                  GmvkqWq+lf+++r +++  + ++ df k aea G    +r+e+p++++  +ke++e ++p++l+v
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 484 CGDGMVKQWQKLFFKGRLAASDRSLHKKDFLKAAEADGFpYVMRLERPQDVARVVKEFVEFQGPAFLEV 552
                                               ************************99************84579************************** PP

                                 TIGR00118 533 evdkeeevlPmvapGagldelve 555
                                                +d ++ v+Pmv pG+  +e+++
  lcl|NCBI__GCF_001579945.1:WP_083537097.1 553 MIDPDAGVYPMVGPGQPYSEMIT 575
                                               ********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (596 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: 9.37
//
[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