GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Shewanella oneidensis MR-1

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 203427 SO4349 ketol-acid reductoisomerase (NCBI ptt file)

Query= BRENDA::A0KS29
         (492 letters)



>FitnessBrowser__MR1:203427
          Length = 492

 Score =  972 bits (2512), Expect = 0.0
 Identities = 482/492 (97%), Positives = 491/492 (99%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIP+ADLVLNLTPDKQHSNVVSAVMP
Sbjct: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPSADLVLNLTPDKQHSNVVSAVMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGATLSYSHGFNIVEEGMQIRPDITV+MVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDPNGDGL+IAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGY+KM
Sbjct: 181 NDPNGDGLDIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLK+ILQPLF
Sbjct: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKDILQPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           EKHMDDIISGEFSRTMMQDWANDDANLLRWRAET ETGFENAPVSSEHIDEQTYFDKGIF
Sbjct: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETGETGFENAPVSSEHIDEQTYFDKGIF 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLFNHAAVP+LRDYVNAMSPEYLGAGLKDSSN+VDNLQLIAINDAIRHT+VEY+GAELR
Sbjct: 421 CYLFNHAAVPLLRDYVNAMSPEYLGAGLKDSSNSVDNLQLIAINDAIRHTAVEYVGAELR 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: 981
Number of extensions: 12
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 203427 SO4349 (ketol-acid reductoisomerase (NCBI ptt file))
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.17966.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-134  434.2   0.1   1.4e-124  401.1   0.0    2.1  2  lcl|FitnessBrowser__MR1:203427  SO4349 ketol-acid reductoisomera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203427  SO4349 ketol-acid reductoisomerase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  401.1   0.0  1.4e-124  1.4e-124       2     312 ..      36     367 ..      35     369 .. 0.97
   2 !   37.1   0.0     9e-14     9e-14     185     248 ..     361     424 ..     359     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 401.1 bits;  conditional E-value: 1.4e-124
                       TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqkev 75 
                                     k+ +++i+G+G+qG +q+ln+rdsgln+ ++lr+ea     asw+kA+++Gfkv t+ee+i++adl+++L+pD+ q+++
  lcl|FitnessBrowser__MR1:203427  36 KDWNIVILGCGAQGLNQGLNMRDSGLNIAYALRPEAiaqkrASWQKATDNGFKVGTFEELIPSADLVLNLTPDK-QHSN 113
                                     7789*******************************999999*********************************.7777 PP

                       TIGR00465  76 yeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeakeiAl 152
                                     ++  ++pl+k+g++l++sHGfniv+++++i+ d++v++vAPK+pG++vReeyk+g+Gvp+liAv+++  ++g++ +iA+
  lcl|FitnessBrowser__MR1:203427 114 VVSAVMPLMKQGATLSYSHGFNIVEEGMQIRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPNGDGLDIAK 192
                                     7777************************************************************988779********* PP

                       TIGR00465 153 ayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGle 231
                                     ayA a+Gg ragvl+++F +Ev+sDL+GEq++LcG+l+ +  ++++++v++G +p +A ++i++++++++++lk++G++
  lcl|FitnessBrowser__MR1:203427 193 AYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKMVADGVEPGYAAKLIQQGWETVTEALKHGGIT 271
                                     ******************************************************************************* PP

                       TIGR00465 232 lmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeearkke...k 295
                                     +m+d++sn+Ak++a+e +e lk+ l++ ++k++++i++Gef++    +wa+++        e+g++ fe+a+ +     
  lcl|FitnessBrowser__MR1:203427 272 NMMDRLSNPAKIKAFEIAEDLKDILQPLFEKHMDDIISGEFSRtmmqDWANDDanllrwraETGETGFENAPVSSehiD 350
                                     *******************************************9999*****9*****************997766889 PP

                       TIGR00465 296 eqeiekvGkelralvka 312
                                     eq ++++G  l a++ka
  lcl|FitnessBrowser__MR1:203427 351 EQTYFDKGIFLVAMIKA 367
                                     **************987 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 9e-14
                       TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalel 248
                                     L+ +++a++++afdt+v aG  +e Ay e +he  li++ + +k l +m   +s+tA++g +  
  lcl|FitnessBrowser__MR1:203427 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCYLF 424
                                     889*********************************************************8754 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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 2.20
//
[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