Alignments for a candidate for ilvC in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Shewanella loihica PV-4

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 5207767 Shew_0288 ketol-acid reductoisomerase (RefSeq)

Query= BRENDA::A0KS29
         (492 letters)



>FitnessBrowser__PV4:5207767
          Length = 493

 Score =  895 bits (2312), Expect = 0.0
 Identities = 439/490 (89%), Positives = 466/490 (95%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSLNLRQQL QLGQCRFMDRSEFS GC+YIK WNIVILGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLNLRQQLEQLGQCRFMDRSEFSQGCDYIKGWNIVILGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           LNI++ALR +AIA++R S+QKAT NGF+VGTFEELIP ADLVLNLTPDKQH++ V+AVMP
Sbjct: 61  LNISFALREQAIAEQRPSYQKATGNGFRVGTFEELIPDADLVLNLTPDKQHTDAVNAVMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGA LSYSHGFNIVEEGMQ+RPDITV+MVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGAVLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDP GDGLE+AKAYASATGGDRAGVL SSFIAEVKSDLMGEQTILCGMLQTGAILGY+KM
Sbjct: 181 NDPKGDGLEVAKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VADG+EPGYAAKLIQQGWET TEALKHGGIT+MMDRLSNPAKIKAFE+AE+LK ILQPLF
Sbjct: 241 VADGIEPGYAAKLIQQGWETTTEALKHGGITHMMDRLSNPAKIKAFEMAEELKAILQPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           EKHMDDIISGEFS+TMM+DWANDDANLL+WRAET ETGFENAP   E IDEQTYFDKGIF
Sbjct: 301 EKHMDDIISGEFSKTMMEDWANDDANLLKWRAETNETGFENAPACDEAIDEQTYFDKGIF 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLFNHAAVP+LRDYVN MSPEYLG GLKDS N VDNL+LI +NDAIRHT+VEYIGAELR
Sbjct: 421 CYLFNHAAVPLLRDYVNQMSPEYLGGGLKDSGNGVDNLRLIEVNDAIRHTAVEYIGAELR 480

Query: 481 GYMTDMKSIV 490
           GYMT+MK IV
Sbjct: 481 GYMTEMKRIV 490


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: 928
Number of extensions: 14
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 5207767 Shew_0288 (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.26094.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   7.5e-131  421.7   0.3   8.6e-121  388.7   0.1    2.1  2  lcl|FitnessBrowser__PV4:5207767  Shew_0288 ketol-acid reductoisom


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207767  Shew_0288 ketol-acid reductoisomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.7   0.1  8.6e-121  8.6e-121       2     312 ..      36     367 ..      35     369 .. 0.97
   2 !   37.3   0.0   8.1e-14   8.1e-14     185     249 ..     361     425 ..     359     486 .. 0.88

  Alignments for each domain:
  == domain 1  score: 388.7 bits;  conditional E-value: 8.6e-121
                        TIGR00465   2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 
                                      kg +++i+G+G+qG +q+ln+rdsgln++ +lr++a      s++kA+ +Gf+v t+ee+i++adl+++L+pD+ q++
  lcl|FitnessBrowser__PV4:5207767  36 KGWNIVILGCGAQGLNQGLNMRDSGLNISFALREQAiaeqrPSYQKATGNGFRVGTFEELIPDADLVLNLTPDK-QHT 112
                                      7789*******************************9999999********************************.888 PP

                        TIGR00465  75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeakei 150
                                      + ++ ++pl+k+g++l++sHGfniv+++++++ d++v++vAPK+pG++vReeyk+g+Gvp+liAv+++  ++g++ e+
  lcl|FitnessBrowser__PV4:5207767 113 DAVNAVMPLMKQGAVLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPKGDGLEV 190
                                      88888************************************************************98877******** PP

                        TIGR00465 151 AlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkek 228
                                      A+ayA a+Gg ragvl ++F +Ev+sDL+GEq++LcG+l+ +  ++++++v++G +p +A ++i++++++ +++lk++
  lcl|FitnessBrowser__PV4:5207767 191 AKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKMVADGIEPGYAAKLIQQGWETTTEALKHG 268
                                      ****************************************************************************** PP

                        TIGR00465 229 GlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeearkke 294
                                      G+++m+d++sn+Ak++a+e++e lk+ l++ ++k++++i++Gef+k    +wa+++        e++++ fe+a+  +
  lcl|FitnessBrowser__PV4:5207767 269 GITHMMDRLSNPAKIKAFEMAEELKAILQPLFEKHMDDIISGEFSKtmmeDWANDDanllkwraETNETGFENAPACD 346
                                      **********************************************99999***99*******************999 PP

                        TIGR00465 295 ...keqeiekvGkelralvka 312
                                          eq ++++G  l a++ka
  lcl|FitnessBrowser__PV4:5207767 347 eaiDEQTYFDKGIFLVAMIKA 367
                                      8999**************987 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 8.1e-14
                        TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr 249
                                      L+ +++a++++afdt+v aG  +e Ay e +he  li++ + +k l +m   +s+tA++g +  +
  lcl|FitnessBrowser__PV4:5207767 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCYLFN 425
                                      889*********************************************************87655 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: 0.05u 0.00s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 3.39
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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