Alignments for a candidate for ilvC in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvC in Pedobacter sp. GW460-11-11-14-LB5

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate CA265_RS15825 CA265_RS15825 ketol-acid reductoisomerase

Query= BRENDA::P05793
         (491 letters)



>FitnessBrowser__Pedo557:CA265_RS15825
          Length = 493

 Score =  696 bits (1796), Expect = 0.0
 Identities = 353/493 (71%), Positives = 400/493 (81%), Gaps = 3/493 (0%)

Query: 1   MANYFNTLNLRQQLAQLGKCRFMGRDEFADGASYLQGKKVVIVGCGAQGLNQGLNMRDSG 60
           MANYFNTL LR++L QLG C FM   EF DG + L+GKK+VIVGCGAQGLNQGLN+RDSG
Sbjct: 1   MANYFNTLPLREKLNQLGVCDFMDSSEFLDGVNALKGKKLVIVGCGAQGLNQGLNLRDSG 60

Query: 61  LDISYALRKEAIAEKRASWRKATENGFKVGTYEELIPQADLVINLTPDKQHSDVVRTVQP 120
           LD+SY LRKEAI  KR SW+ ATEN F VGTYEELIP AD+VINLTPDKQH+ VV  + P
Sbjct: 61  LDVSYTLRKEAIEGKRDSWKNATENNFTVGTYEELIPNADVVINLTPDKQHTAVVNAIMP 120

Query: 121 LMKDGAALGYSHGFNIVEVGEQIRKDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMK+GA L YSHGFNIVE G QIRKD+TV+MVAPKCPG+EVR EY RGFGVPTLIAVHPE
Sbjct: 121 LMKEGATLLYSHGFNIVEEGMQIRKDLTVIMVAPKCPGSEVRAEYVRGFGVPTLIAVHPE 180

Query: 181 NDPKGEGMAIAKAWAAATGGHRAGVLESSFVAEVKSDLMGEQTILCGMLQAGSLLCFDKL 240
           NDP+G+G+A AKA+ A TGGHRAGVL+SSFVAEVKSDLMGEQTILCG+LQ GS+L FDK+
Sbjct: 181 NDPQGKGLAQAKAYCAGTGGHRAGVLKSSFVAEVKSDLMGEQTILCGLLQTGSILSFDKM 240

Query: 241 VEEGTDPAYAEKLIQFGWETITEALKQGGITLMMDRLSNPAKLRAYALSEQLKEIMAPLF 300
           VE+G D  YA KL+Q+G E ITEALKQGGIT MMDRLSN AK++A+ +SE+LK+IM PLF
Sbjct: 241 VEKGIDAGYASKLVQYGVEVITEALKQGGITAMMDRLSNVAKIKAFEISEELKDIMRPLF 300

Query: 301 QKHMDDIISGEFSSGMMADWANDDKKLLTWREETGKTAFETAPQYEGKIGEQEYFDKGVL 360
           QKH DDI+SGEFS  MM DWAN DK LL WR ETG+TAFE  P  + KIGEQEYFD   L
Sbjct: 301 QKHQDDIMSGEFSRTMMEDWANGDKNLLKWRAETGETAFEKTPAGDVKIGEQEYFDNYTL 360

Query: 361 MIAMVKAGVELAFETMVDSGIIEESAYYESLHELPLIANTIARKRLYEMNVVISDTAEYG 420
           M+A V+AGVELAFETMV +GI  ESAYYESLHE PLIANTIARK+L+EMN VISDTAEYG
Sbjct: 361 MVAFVRAGVELAFETMVQAGIKPESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYG 420

Query: 421 NYLFSYACVPLLKPFMAELQPGDLGKAIPE---GAVDNGQLRDVNEAIRSHAIEQVGKKL 477
            YLF  AC PLL  FM ++    +GK   E   GAVDN +L D+NEAIRSH +EQ+G  L
Sbjct: 421 CYLFDQACKPLLGDFMKKVDTDLVGKNFNEGKDGAVDNRKLIDINEAIRSHEVEQIGATL 480

Query: 478 RGYMTDMKRIAVA 490
           R  MT MK I  A
Sbjct: 481 RKAMTAMKAIKTA 493


Lambda     K      H
   0.317    0.135    0.390 

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: 748
Number of extensions: 25
Number of successful extensions: 3
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: 491
Length of database: 493
Length adjustment: 34
Effective length of query: 457
Effective length of database: 459
Effective search space:   209763
Effective search space used:   209763
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 CA265_RS15825 CA265_RS15825 (ketol-acid reductoisomerase)
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.18390.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.5e-135  435.6   2.5   5.7e-120  386.0   0.5    2.0  2  lcl|FitnessBrowser__Pedo557:CA265_RS15825  CA265_RS15825 ketol-acid reducto


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15825  CA265_RS15825 ketol-acid reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.0   0.5  5.7e-120  5.7e-120       1     310 [.      35     365 ..      35     367 .. 0.97
   2 !   52.2   0.1   2.2e-18   2.2e-18     182     313 ..     358     487 ..     351     488 .. 0.80

  Alignments for each domain:
  == domain 1  score: 386.0 bits;  conditional E-value: 5.7e-120
                                  TIGR00465   1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadli 63 
                                                lkgkk++i+G+G+qG +q+lnlrdsgl+v+++lrkea      swk+A+e+ f v t+ee+i++ad++
  lcl|FitnessBrowser__Pedo557:CA265_RS15825  35 LKGKKLVIVGCGAQGLNQGLNLRDSGLDVSYTLRKEAiegkrDSWKNATENNFTVGTYEELIPNADVV 102
                                                79***********************************999999************************* PP

                                  TIGR00465  64 miLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegr 131
                                                ++L+pD+ q++ +++ i+pl+keg++ll+sHGfniv+++++i+kd++v++vAPK+pG++vR ey +g+
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 103 INLTPDK-QHTAVVNAIMPLMKEGATLLYSHGFNIVEEGMQIRKDLTVIMVAPKCPGSEVRAEYVRGF 169
                                                *******.77777777**************************************************** PP

                                  TIGR00465 132 GvpsliAveqd..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaaf 197
                                                Gvp+liAv+++  ++g++ ++A+ay +++Gg+ragvl+++F++Ev+sDL+GEq++LcG l+ ++ ++f
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 170 GVPTLIAVHPEndPQGKGLAQAKAYCAGTGGHRAGVLKSSFVAEVKSDLMGEQTILCGLLQTGSILSF 237
                                                ********988779****************************************************** PP

                                  TIGR00465 198 dtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilk 265
                                                d++ve+G +  +A +++++++++i+++lk++G++ m+d++sn Ak++a+e +e lk+ +++ +qk+ +
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 238 DKMVEKGIDAGYASKLVQYGVEVITEALKQGGITAMMDRLSNVAKIKAFEISEELKDIMRPLFQKHQD 305
                                                ******************************************************************** PP

                                  TIGR00465 266 eiqnGefak....ewalek........eagkpafeearkke...keqeiekvGkelralv 310
                                                +i +Gef++    +wa+++        e+g++afe+++  +    eqe++++   + a v
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 306 DIMSGEFSRtmmeDWANGDknllkwraETGETAFEKTPAGDvkiGEQEYFDNYTLMVAFV 365
                                                *********999999999999*****99**********9999899*****9988888765 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 2.2e-18
                                  TIGR00465 182 qavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr 249
                                                 + ++  ++a++++af+t+v+aG +pe Ay e +he  li++ + +k l +m + +s+tA++g +   
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 358 YTLMVAFVRAGVELAFETMVQAGIKPESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYGCYLFD 425
                                                567788899******************************************************99766 PP

                                  TIGR00465 250 eilkeelkkemqkilkeiqnGefakewalek..eagkpafeearkkekeqeiekvGkelralvkae 313
                                                +  k  l   m+k+  ++      k++  +k  ++++ ++ +++++ + +e+e++G +lr+ + a 
  lcl|FitnessBrowser__Pedo557:CA265_RS15825 426 QACKPLLGDFMKKVDTDL----VGKNFNEGKdgAVDNRKLIDINEAIRSHEVEQIGATLRKAMTAM 487
                                                666666665555555555....4444433332256667788888888*************998765 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.25
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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