GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Shewanella sp. ANA-3

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 7023117 Shewana3_0355 ketol-acid reductoisomerase (RefSeq)

Query= BRENDA::A0KS29
         (492 letters)



>FitnessBrowser__ANA3:7023117
          Length = 492

 Score =  984 bits (2543), Expect = 0.0
 Identities = 492/492 (100%), Positives = 492/492 (100%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP
Sbjct: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM
Sbjct: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF
Sbjct: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF
Sbjct: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR
Sbjct: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480

Query: 481 GYMTDMKSIVGA 492
           GYMTDMKSIVGA
Sbjct: 481 GYMTDMKSIVGA 492


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: 986
Number of extensions: 11
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: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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 7023117 Shewana3_0355 (ketol-acid reductoisomerase (RefSeq))
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.619604.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.7e-135  435.2   0.2     8e-125  401.9   0.0    2.1  2  lcl|FitnessBrowser__ANA3:7023117  Shewana3_0355 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023117  Shewana3_0355 ketol-acid reductoisomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.9   0.0    8e-125    8e-125       2     312 ..      36     367 ..      35     369 .. 0.97
   2 !   38.9   0.1   2.5e-14   2.5e-14     183     249 ..     359     425 ..     331     486 .. 0.81

  Alignments for each domain:
  == domain 1  score: 401.9 bits;  conditional E-value: 8e-125
                         TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                       k+ +++i+G+G+qG +q+ln+rdsgln+ ++lr+ea     asw+kA+++Gfkv t+ee+i++adl+++L+pD+ q+
  lcl|FitnessBrowser__ANA3:7023117  36 KDWNIVILGCGAQGLNQGLNMRDSGLNIAYALRPEAiaqkrASWQKATDNGFKVGTFEELIPTADLVLNLTPDK-QH 111
                                       7789*******************************999999*********************************.77 PP

                         TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeak 148
                                       ++++  ++pl+k+g++l++sHGfniv+++++i+ d++vv+vAPK+pG++vReeyk+g+Gvp+liAv+++  ++g++ 
  lcl|FitnessBrowser__ANA3:7023117 112 SNVVSAVMPLMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPNGDGL 188
                                       777777************************************************************988779***** PP

                         TIGR00465 149 eiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdll 225
                                       eiA+ayA a+Gg ragvl+++F +Ev+sDL+GEq++LcG+l+ +  +++d++v++G +p +A ++i++++++++++l
  lcl|FitnessBrowser__ANA3:7023117 189 EIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKMVADGVEPGYAAKLIQQGWETVTEAL 265
                                       ***************************************************************************** PP

                         TIGR00465 226 kekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeea 290
                                       k++G+++m+d++sn+Ak++a+e +e lke l++ ++k++++i++Gef++    +wa+++        e++++ fe+a
  lcl|FitnessBrowser__ANA3:7023117 266 KHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLFEKHMDDIISGEFSRtmmqDWANDDanllrwraETAETGFENA 342
                                       *************************************************9999*****9******999999***999 PP

                         TIGR00465 291 rkke...keqeiekvGkelralvka 312
                                       + +     eq ++++G  l a++ka
  lcl|FitnessBrowser__ANA3:7023117 343 PVSSehiDEQTYFDKGIFLVAMIKA 367
                                       87766889**************987 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 2.5e-14
                         TIGR00465 183 avLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr 249
                                         L+ +++a++++afdt+v aG  +e Ay e +he  li++ + +k l +m   +s+tA++g +  +
  lcl|FitnessBrowser__ANA3:7023117 359 IFLVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCYLFN 425
                                       36999*********************************************************87554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (492 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.54
//
[ok]

This GapMind analysis is from Apr 09 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:

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