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

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.17870.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 4.02
//
[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:

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