GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Shewanella amazonensis SB2B

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 6939188 Sama_3282 ketol-acid reductoisomerase (RefSeq)

Query= BRENDA::A0KS29
         (492 letters)



>FitnessBrowser__SB2B:6939188
          Length = 493

 Score =  885 bits (2286), Expect = 0.0
 Identities = 439/492 (89%), Positives = 462/492 (93%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSLNLRQQLAQL QCRFMDRSEF +GC+YIK WNIVILGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLNLRQQLAQLSQCRFMDRSEFENGCDYIKGWNIVILGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           LNI+YALR EAIA+KRASW+KATDNGF VGTFEELIP ADLVLNLTPDKQHSNVV+ VMP
Sbjct: 61  LNISYALRAEAIAEKRASWKKATDNGFTVGTFEELIPQADLVLNLTPDKQHSNVVNTVMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGATLSYSHGFNIVEEGMQ+RPDITV+MVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGATLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDP GDGLEIAKAYASATGGDRAGVL SSFIAEVKSDLMGEQTILCGMLQT AILGY+KM
Sbjct: 181 NDPRGDGLEIAKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTSAILGYEKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VADGVEPGYAAKLIQQG ET+TEALK GGITNMMDRLSNPAKIKAF++AE+LK IL PLF
Sbjct: 241 VADGVEPGYAAKLIQQGLETITEALKQGGITNMMDRLSNPAKIKAFDMAEELKGILAPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           EKHMDDIISGEFSRTMM DWANDDANLLRWRAET ET FENAP S+EHIDEQTYFDKGIF
Sbjct: 301 EKHMDDIISGEFSRTMMADWANDDANLLRWRAETNETAFENAPSSNEHIDEQTYFDKGIF 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           LVAMIKAGVELAFDTMV AGI+EESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 LVAMIKAGVELAFDTMVDAGIIEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLFNHAAVP+LRDYV +MS EYLG GLKDSSN VDN++LI +N AIR+T+VE+IG ELR
Sbjct: 421 CYLFNHAAVPLLRDYVKSMSAEYLGGGLKDSSNAVDNVRLIEVNQAIRNTAVEFIGEELR 480

Query: 481 GYMTDMKSIVGA 492
           GYM DMK I  A
Sbjct: 481 GYMKDMKRISAA 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: 903
Number of extensions: 17
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: 493
Length adjustment: 34
Effective length of query: 458
Effective length of database: 459
Effective search space:   210222
Effective search space used:   210222
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 6939188 Sama_3282 (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.23983.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-135  437.5   0.2   2.5e-124  400.3   0.0    2.0  2  lcl|FitnessBrowser__SB2B:6939188  Sama_3282 ketol-acid reductoisom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939188  Sama_3282 ketol-acid reductoisomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.3   0.0  2.5e-124  2.5e-124       2     312 ..      36     367 ..      35     368 .. 0.98
   2 !   40.9   0.0   6.3e-15   6.3e-15     185     311 ..     361     484 ..     359     487 .. 0.86

  Alignments for each domain:
  == domain 1  score: 400.3 bits;  conditional E-value: 2.5e-124
                         TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 
                                       kg +++i+G+G+qG +q+ln+rdsgln++++lr ea     aswkkA+++Gf v t+ee+i++adl+++L+pD+ q+
  lcl|FitnessBrowser__SB2B:6939188  36 KGWNIVILGCGAQGLNQGLNMRDSGLNISYALRAEAiaekrASWKKATDNGFTVGTFEELIPQADLVLNLTPDK-QH 111
                                       7789*******************************999*99*********************************.88 PP

                         TIGR00465  74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeak 148
                                       ++++++++pl+k+g++l++sHGfniv+++++++ d++v++vAPK+pG++vReeyk+g+Gvp+liAv+++  + g++ 
  lcl|FitnessBrowser__SB2B:6939188 112 SNVVNTVMPLMKQGATLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPRGDGL 188
                                       889999************************************************************988779***** PP

                         TIGR00465 149 eiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdll 225
                                       eiA+ayA a+Gg ragvl ++F +Ev+sDL+GEq++LcG+l+    ++++++v++G +p +A ++i+++l++i+++l
  lcl|FitnessBrowser__SB2B:6939188 189 EIAKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTSAILGYEKMVADGVEPGYAAKLIQQGLETITEAL 265
                                       ***************************************************************************** PP

                         TIGR00465 226 kekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeea 290
                                       k++G+++m+d++sn+Ak++a++++e lk  l++ ++k++++i++Gef++    +wa+++        e++++afe+a
  lcl|FitnessBrowser__SB2B:6939188 266 KQGGITNMMDRLSNPAKIKAFDMAEELKGILAPLFEKHMDDIISGEFSRtmmaDWANDDanllrwraETNETAFENA 342
                                       *************************************************9999*****9****************** PP

                         TIGR00465 291 rkke...keqeiekvGkelralvka 312
                                       + ++    eq ++++G  l a++ka
  lcl|FitnessBrowser__SB2B:6939188 343 PSSNehiDEQTYFDKGIFLVAMIKA 367
                                       99888999**************986 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 6.3e-15
                         TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemq 261
                                       L+ +++a++++afdt+v+aG  +e Ay e +he  li++ + +k l +m   +s+tA++g +  ++     l+  ++
  lcl|FitnessBrowser__SB2B:6939188 361 LVAMIKAGVELAFDTMVDAGIIEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCYLFNHAAVPLLRDYVK 437
                                       889**********************************************************9988888888887777 PP

                         TIGR00465 262 kilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvk 311
                                        +  e   G         +++++ ++ e +++ +++ +e +G+elr  +k
  lcl|FitnessBrowser__SB2B:6939188 438 SMSAEYLGGGLKD---SSNAVDNVRLIEVNQAIRNTAVEFIGEELRGYMK 484
                                       7777766666544...3445678899999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (314 nodes)
Target sequences:                          1  (493 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 3.73
//
[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