Alignments for a candidate for ilvI in Rhodospirillum centenum SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Rhodospirillum centenum SW; ATCC 51521

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012567154.1 RC1_RS09480 acetolactate synthase 3 large subunit

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



>NCBI__GCF_000016185.1:WP_012567154.1
          Length = 596

 Score =  652 bits (1683), Expect = 0.0
 Identities = 326/571 (57%), Positives = 413/571 (72%), Gaps = 6/571 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           ++ GAEI++ AL ++GV+ ++GYPGGAVL IYD L KQ +  HILVRHEQAAVHAA+GYA
Sbjct: 14  KLTGAEIVIKALRDQGVDVIFGYPGGAVLPIYDALFKQNEIRHILVRHEQAAVHAAEGYA 73

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGKVGV LVTSGPG TNAVTG+  A +DSIP+V +TG VPTH IG DAFQECDT GIT
Sbjct: 74  RSTGKVGVVLVTSGPGATNAVTGLVDALMDSIPVVCLTGQVPTHLIGNDAFQECDTTGIT 133

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVK V +LA TI + F++A  GRPGPVV+DIPKDV      Y  P     +S
Sbjct: 134 RPASKHNYLVKHVDNLARTIHEGFYVARNGRPGPVVIDIPKDVQFAEGPYRTPGECAPKS 193

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255
           Y P  +    ++ +AV L+  A RP  Y GGGV+ +   AS  L QL  +TG+P T TLM
Sbjct: 194 YRPQIRPDLNRVEEAVELIANARRPIFYVGGGVINSGPIASQLLTQLVRMTGYPCTTTLM 253

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGAFP +  QF+GMLGMHGTYEAN+AM  CDV+I IGARFDDRV G  + F   ++K I
Sbjct: 254 GLGAFPASDPQFLGMLGMHGTYEANLAMHGCDVMINIGARFDDRVTGKLSEFAPGSKK-I 312

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           H+DIDPSSI+K V VD+ IVG+   VL+++I   KA   +P REALA WW+QIE WR+ D
Sbjct: 313 HVDIDPSSINKNVPVDVAIVGDAAHVLEDMIRLWKARAKQPDREALAAWWKQIEGWRARD 372

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG--DAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433
           CL+Y+++ ++IKPQY +E++ ELT+G  D FI ++VGQHQMWAAQF  F++P RW+ SGG
Sbjct: 373 CLRYEKTDKVIKPQYALERLRELTRGRDDVFITTEVGQHQMWAAQFLPFEKPNRWLTSGG 432

Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493
           LGTMG GLP A+G++ A P+  VV + GE SI M IQE+ST LQY  PVK+  LNN ++G
Sbjct: 433 LGTMGYGLPAAIGVQIAHPKALVVDVAGEASILMNIQEMSTALQYRLPVKVFILNNQWMG 492

Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553
           MVRQWQ++ +  RYS SY  ALPDFVKLAEA+G VG+R  K S+V+  +R       + V
Sbjct: 493 MVRQWQQLLHGERYSESYSQALPDFVKLAEAFGAVGLRATKVSEVDDVIRTMIE-TPKAV 551

Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584
            +D   D  EN +PM+  GK  +EMLLG E+
Sbjct: 552 IVDMCVDQKENCFPMIPGGKAHNEMLLGPEE 582


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: 954
Number of extensions: 35
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_012567154.1 RC1_RS09480 (acetolactate synthase 3 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.12347.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-245  802.3   0.0   1.3e-245  802.0   0.0    1.0  1  lcl|NCBI__GCF_000016185.1:WP_012567154.1  RC1_RS09480 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016185.1:WP_012567154.1  RC1_RS09480 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  802.0   0.0  1.3e-245  1.3e-245       1     554 [.      15     577 ..      15     580 .. 0.97

  Alignments for each domain:
  == domain 1  score: 802.0 bits;  conditional E-value: 1.3e-245
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gaei++++l+++gv+++fGyPGGavlpiydal+ ++e++hilvrheqaa+haa+Gyar++GkvGvvl
  lcl|NCBI__GCF_000016185.1:WP_012567154.1  15 LTGAEIVIKALRDQGVDVIFGYPGGAVLPIYDALFkQNEIRHILVRHEQAAVHAAEGYARSTGKVGVVL 83 
                                               68*********************************999******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn+vtg+++a +ds+P+v ltGqv+t+liG+dafqe+d +Git+p  kh++lvk++++l+++
  lcl|NCBI__GCF_000016185.1:WP_012567154.1  84 VTSGPGATNAVTGLVDALMDSIPVVCLTGQVPTHLIGNDAFQECDTTGITRPASKHNYLVKHVDNLART 152
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206
                                               ++e f++a  GrPGPv++d+Pkdv+ ae  ++++ +   ++y+p+++++ +++++a+eli++a++P+ +
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 153 IHEGFYVARNGRPGPVVIDIPKDVQFAEGPYRTPGECAPKSYRPQIRPDLNRVEEAVELIANARRPIFY 221
                                               ********************************************************************* PP

                                 TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               vGgGvi ++  as+ l++l+ ++  p tttl+GlGafp+ +p++lgmlGmhGt+eanla++ +d++i +
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 222 VGGGVINSGpiASQLLTQLVRMTGYPCTTTLMGLGAFPASDPQFLGMLGMHGTYEANLAMHGCDVMINI 290
                                               ******99766899******************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrvtg+l++fap +k ih+didP++i+knv vd++ivGda +vle++++  k++    +++   
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 291 GARFDDRVTGKLSEFAPGSKKIHVDIDPSSINKNVPVDVAIVGDAAHVLEDMIRLWKARakqpDREALA 359
                                               ****************************************************98777665454444444 PP

                                 TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd..eaivttdvGqhqmwaaqfyktkkprkfi 404
                                                W+++ie w+++ +l+++++++ ikPq+ +++l +l+++  ++++tt+vGqhqmwaaqf++++kp++++
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 360 aWWKQIEGWRARDCLRYEKTDKVIKPQYALERLRELTRGrdDVFITTEVGQHQMWAAQFLPFEKPNRWL 428
                                               7***********************************987669*************************** PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               tsgGlGtmG+GlPaa+G+++a+p++ vv+v+G++s+ mn+qe+st+ +y +pvk+ ilnn+++Gmv+qW
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 429 TSGGLGTMGYGLPAAIGVQIAHPKALVVDVAGEASILMNIQEMSTALQYRLPVKVFILNNQWMGMVRQW 497
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542
                                               q+l++ eryse++ ++ lpdfvklaea+G++g+r +k +e+++ ++ ++e+ + v++d+ vd++e+++P
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 498 QQLLHGERYSESYSQA-LPDFVKLAEAFGAVGLRATKVSEVDDVIRTMIETPKAVIVDMCVDQKENCFP 565
                                               *************995.**************************************************** PP

                                 TIGR00118 543 mvapGagldelv 554
                                               m++ G++ +e++
  lcl|NCBI__GCF_000016185.1:WP_012567154.1 566 MIPGGKAHNEML 577
                                               **********97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.97
//
[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