Alignments for a candidate for ilvC in Shewanella amazonensis SB2B

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.23456.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: 00:00:00.05
# Mc/sec: 2.97
//
[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