GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Flavobacterium glycines Gm-149

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate WP_066325987.1 BLR17_RS13770 ketol-acid reductoisomerase

Query= BRENDA::A0KS29
         (492 letters)



>NCBI__GCF_900100165.1:WP_066325987.1
          Length = 490

 Score =  732 bits (1890), Expect = 0.0
 Identities = 361/490 (73%), Positives = 411/490 (83%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSL LR QL QLG C FMD+SEF++G   +K   +VI+GCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLPLRLQLEQLGVCEFMDQSEFANGIEALKGKKVVIVGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           L+I+YALR EAIAQKRAS+  A DNGF VGT+EELIPTADLV NLTPDKQH+ VV+A+MP
Sbjct: 61  LDISYALRAEAIAQKRASFMNAADNGFNVGTYEELIPTADLVCNLTPDKQHTAVVTAIMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGATL+YSHGFNIVEEGMQIR D+TV+M APKCPG+EVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGATLAYSHGFNIVEEGMQIRKDLTVIMCAPKCPGSEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDPNG GL+ AKAYA ATGG RAGVL+SSF+AEVKSDLMGEQTILCG+LQTG+IL +DKM
Sbjct: 181 NDPNGFGLDQAKAYAVATGGHRAGVLRSSFVAEVKSDLMGEQTILCGLLQTGSILCFDKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VA+GVEPGYA+KLIQ GWET+TE LKHGGITNMMDRLSNPAKI AF  AE+LK+I++PLF
Sbjct: 241 VAEGVEPGYASKLIQYGWETITEGLKHGGITNMMDRLSNPAKIAAFNAAEELKDIMRPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           +KHMDDIISG FS+TMM+DWANDD NLL WRA TAET FE  P     I EQ Y+D G  
Sbjct: 301 QKHMDDIISGHFSKTMMEDWANDDKNLLTWRAATAETNFEKTPAGDMEISEQEYYDNGTL 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           +VAM+KAGVELAF+ M  +GI+EESAYYESLHETPLIANTIARK+L+EMN VISDTAEYG
Sbjct: 361 MVAMVKAGVELAFEAMTDSGIIEESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLF+HA  P++ DYV       +G    + SN VDN +LI +N  IR+  VE +GA LR
Sbjct: 421 CYLFDHACKPLIADYVKNAPSNLVGRPFSNGSNGVDNKELIDVNSIIRNHPVEEVGAWLR 480

Query: 481 GYMTDMKSIV 490
             MT MK IV
Sbjct: 481 ESMTAMKKIV 490


Lambda     K      H
   0.317    0.134    0.389 

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: 801
Number of extensions: 19
Number of successful extensions: 1
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: 492
Length of database: 490
Length adjustment: 34
Effective length of query: 458
Effective length of database: 456
Effective search space:   208848
Effective search space used:   208848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_066325987.1 BLR17_RS13770 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

# 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/TIGR00465.hmm
# target sequence database:        /tmp/gapView.289019.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00465  [M=314]
Accession:   TIGR00465
Description: ilvC: ketol-acid reductoisomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-135  436.5   0.1   7.2e-126  405.3   0.1    2.0  2  NCBI__GCF_900100165.1:WP_066325987.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066325987.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.1  7.2e-126  7.2e-126       1     312 [.      35     367 ..      35     369 .. 0.97
   2 !   35.7   0.0   2.5e-13   2.5e-13     185     312 ..     361     485 ..     359     487 .. 0.86

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 7.2e-126
                             TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlp 68 
                                           lkgkkv+i+G+G+qG +q+ln+rdsgl+++++lr ea     as+ +A ++Gf+v t+ee+i++adl+ +L+p
  NCBI__GCF_900100165.1:WP_066325987.1  35 LKGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRAEAiaqkrASFMNAADNGFNVGTYEELIPTADLVCNLTP 107
                                           79**********************************999999******************************* PP

                             TIGR00465  69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveq 141
                                           D+ q++ ++  i+pl+k+g++l +sHGfniv+++++i+kd++v++ APK+pG++vReeyk+g+Gvp+liAv++
  NCBI__GCF_900100165.1:WP_066325987.1 108 DK-QHTAVVTAIMPLMKQGATLAYSHGFNIVEEGMQIRKDLTVIMCAPKCPGSEVREEYKRGFGVPTLIAVHP 179
                                           **.77777777************************************************************98 PP

                             TIGR00465 142 d..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyf 212
                                           +  ++g + ++A+ayA+a+Gg+ragvl ++F++Ev+sDL+GEq++LcG l+ ++ ++fd++v++G +p +A +
  NCBI__GCF_900100165.1:WP_066325987.1 180 EndPNGFGLDQAKAYAVATGGHRAGVLRSSFVAEVKSDLMGEQTILCGLLQTGSILCFDKMVAEGVEPGYASK 252
                                           87799******************************************************************** PP

                             TIGR00465 213 eivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek. 280
                                           +i++++++i++ lk++G+++m+d++sn+Ak+ a++++e lk+ +++ +qk++++i++G+f+k    +wa+++ 
  NCBI__GCF_900100165.1:WP_066325987.1 253 LIQYGWETITEGLKHGGITNMMDRLSNPAKIAAFNAAEELKDIMRPLFQKHMDDIISGHFSKtmmeDWANDDk 325
                                           **************************************************************99999***999 PP

                             TIGR00465 281 .......eagkpafeearkke...keqeiekvGkelralvka 312
                                                  ++++++fe+++  +   +eqe++++G  + a+vka
  NCBI__GCF_900100165.1:WP_066325987.1 326 nlltwraATAETNFEKTPAGDmeiSEQEYYDNGTLMVAMVKA 367
                                           *****999999*****99988889****************97 PP

  == domain 2  score: 35.7 bits;  conditional E-value: 2.5e-13
                             TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelk 257
                                           ++ +++a++++af+ +++ G  +e Ay e +he  li++ + +k l +m + +s+tA++g +     ++++ k
  NCBI__GCF_900100165.1:WP_066325987.1 361 MVAMVKAGVELAFEAMTDSGIIEESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYGCY----LFDHACK 429
                                           6789********************************************************98....5677778 PP

                             TIGR00465 258 kemqkilkeiqnGefakewalek.eagkpafeearkkekeqeiekvGkelralvka 312
                                           + + + +k+  +    + +++++  +++ ++ + +   +++ +e+vG  lr+ + a
  NCBI__GCF_900100165.1:WP_066325987.1 430 PLIADYVKNAPSNLVGRPFSNGSnGVDNKELIDVNSIIRNHPVEEVGAWLRESMTA 485
                                           88888888888888888887775245667788888888999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (490 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: 6.07
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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