Alignments for a candidate for leuA in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Klebsiella michiganensis M5al

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate BWI76_RS22105 BWI76_RS22105 2-isopropylmalate synthase

Query= SwissProt::P06208
         (619 letters)



>FitnessBrowser__Koxy:BWI76_RS22105
          Length = 558

 Score =  544 bits (1402), Expect = e-159
 Identities = 279/571 (48%), Positives = 384/571 (67%), Gaps = 17/571 (2%)

Query: 31  MLKDPSSKYKPFNAPKLSNRKWPDNRITRAPRWLSTDLRDGNQSLPDPMSVEQKKEYFHK 90
           ML  P  KY+P+    L +R+WP+ +ITRAPRWLSTDLRDGNQ+L +PM   +K +++  
Sbjct: 1   MLTQPGEKYRPYPPIALPDRRWPEQQITRAPRWLSTDLRDGNQALAEPMDSARKLQFWDL 60

Query: 91  LVNIGFKEIEVSFPSASQTDFDFTRYAVENA--PDDVSIQCLVQSREHLIKRTVEALTGA 148
           L+  GFKEIEV+FPSASQTDF+F R  +E    P DV+IQ L Q+RE LI RT E+L  A
Sbjct: 61  LLECGFKEIEVAFPSASQTDFNFVRQLIEERRIPQDVTIQVLTQAREDLILRTFESLRDA 120

Query: 149 KKATIHTYLATSDMFREIVFNMSREEAISKAVEATKLVRKLTKDDPSQQATRWSYEFSPE 208
            +AT+H Y AT+ +FRE VF M++ + +  A  AT+L+R+  +  P    TRW YE+SPE
Sbjct: 121 HRATVHLYNATAPLFRERVFGMNKAQVVELATRATRLIRQRCEQQPQ---TRWQYEYSPE 177

Query: 209 CFSDTPGEFAVEICEAVKKAWEPTEENPIIFNLPATVEVASPNVYADQIEYFATHITERE 268
            F  T  EFA+EICEAV + W+P  E P+I NLPATVEV +PNVYADQIEYF  H + R 
Sbjct: 178 TFCFTEPEFALEICEAVAEIWQPCAERPMIINLPATVEVNTPNVYADQIEYFCRHFSRRA 237

Query: 269 KVCISTHCHNDRGCGVAATELGMLAGADRVEGCLFGNGERTGNVDLVTVAMNMYTQGVSP 328
            VCIS H HNDRG GVA+ EL ++AGADRVEGCLFGNGERTGNV LVT+AMN+Y+QGV P
Sbjct: 238 DVCISVHPHNDRGTGVASAELAVMAGADRVEGCLFGNGERTGNVCLVTLAMNLYSQGVDP 297

Query: 329 NLDFSDLTSVLDVVERCNKIPVSQRAPYGGDLVVCAFSGSHQDAIKKGFNLQNKKRAQGE 388
            L F+++  V+++VE CN+IPV  R P+ G L   AFSGSHQDAIKKGF+     R  G+
Sbjct: 298 RLRFAEMNRVVEIVESCNQIPVHPRHPWAGSLAYTAFSGSHQDAIKKGFD----ARRPGD 353

Query: 389 TQWRIPYLPLDPKDIGRDYEAVIRVNSQSGKGGAAWVILRSLGLDLPRNMQIEFSSAVQD 448
            +W +PYLP+DP+DIG  YEAVIRVNSQSGK G+AW+I ++ GL LPR +Q +FS  VQ 
Sbjct: 354 -RWEMPYLPIDPQDIGCSYEAVIRVNSQSGKSGSAWLIEQNHGLKLPRALQQDFSLHVQR 412

Query: 449 HADSLGRELKSDEISKLFKEAYNYNDEQYQAISLVNYNVEKFGTERRVFTGQVKVGDQIV 508
             D+ G+E+  + + +LF+  Y    +    ++L++Y  +     +      +++  +  
Sbjct: 413 ETDTHGKEMTHNALWQLFRARYGLVPQ--PPLALLDYQSDSQQDGQLSLQASLRIAGETR 470

Query: 509 DIEGTGNGPISSLVDALSNLLNVRFAVANYTEHSLGSGSSTQAASYIHLSYRRNADNEKA 568
            ++  GNG +S+    LS LL     + +Y EH+LG  S +++ +YI   +  N D+   
Sbjct: 471 RLQSRGNGLLSAAASGLSGLLKQNIVIKDYHEHTLGERSDSRSVAYIRCVF-PNGDS--- 526

Query: 569 YKWGVGVSEDVGDSSVRAIFATINNIIHSGD 599
            +WGVG+  DV  +S++A+   ++   +SG+
Sbjct: 527 -RWGVGIDNDVARASLQALCNAMSAGHYSGE 556


Lambda     K      H
   0.315    0.131    0.379 

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: 794
Number of extensions: 36
Number of successful extensions: 6
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: 619
Length of database: 558
Length adjustment: 37
Effective length of query: 582
Effective length of database: 521
Effective search space:   303222
Effective search space used:   303222
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate BWI76_RS22105 BWI76_RS22105 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

# 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/TIGR00970.hmm
# target sequence database:        /tmp/gapView.18662.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00970  [M=564]
Accession:   TIGR00970
Description: leuA_yeast: 2-isopropylmalate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.5e-233  762.3   0.0   1.8e-233  762.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS22105  BWI76_RS22105 2-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS22105  BWI76_RS22105 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  762.1   0.0  1.8e-233  1.8e-233       1     560 [.       5     549 ..       5     552 .. 0.97

  Alignments for each domain:
  == domain 1  score: 762.1 bits;  conditional E-value: 1.8e-233
                               TIGR00970   1 pskkykpfkaiklsnrkwpdkvitraprwlsvdlrdGnqalidpmsverkkryfkllvriGfkeievgfps 71 
                                             p +ky+p+ +i l++r+wp+++itraprwls+dlrdGnqal +pm+++rk ++++ll++ Gfkeiev+fps
  lcl|FitnessBrowser__Koxy:BWI76_RS22105   5 PGEKYRPYPPIALPDRRWPEQQITRAPRWLSTDLRDGNQALAEPMDSARKLQFWDLLLECGFKEIEVAFPS 75 
                                             789******************************************************************** PP

                               TIGR00970  72 asqtdfdfvreiieqglipddvtiqvltqsreelikrtvealsGakkaivhlynatsdlfrevvfrasree 142
                                             asqtdf+fvr++ie+  ip+dvtiqvltq+re+li rt+e+l+ a++a+vhlynat++lfre vf +++++
  lcl|FitnessBrowser__Koxy:BWI76_RS22105  76 ASQTDFNFVRQLIEERRIPQDVTIQVLTQAREDLILRTFESLRDAHRATVHLYNATAPLFRERVFGMNKAQ 146
                                             *********************************************************************** PP

                               TIGR00970 143 vlalavegsklvrklvkdaaksketrwsfeyspesfsdtelefavevceavkeviepteerpiifnlpatv 213
                                             v++la+ +++l+r+  ++   +++trw++eyspe+f+ te+efa+e+ceav e+++p++erp+i nlpatv
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 147 VVELATRATRLIRQRCEQ---QPQTRWQYEYSPETFCFTEPEFALEICEAVAEIWQPCAERPMIINLPATV 214
                                             *********999998876...678*********************************************** PP

                               TIGR00970 214 evatpnvyadsieylstniaerekvilslhphndrGtavaaaelGllaGadrieGclfGnGertGnvdlvt 284
                                             ev tpnvyad+iey++++++ r  v++s+hphndrGt+va+ael ++aGadr+eGclfGnGertGnv+lvt
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 215 EVNTPNVYADQIEYFCRHFSRRADVCISVHPHNDRGTGVASAELAVMAGADRVEGCLFGNGERTGNVCLVT 285
                                             *********************************************************************** PP

                               TIGR00970 285 lalnlytqGvspnldfsdldeilrvvercnkipvherhpygGdlvvtafsGshqdaikkGldaldkkkaaa 355
                                             la+nly+qGv+p+l f++++ ++++ve+cn+ipvh+rhp++G l +tafsGshqdaikkG+da        
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 286 LAMNLYSQGVDPRLRFAEMNRVVEIVESCNQIPVHPRHPWAGSLAYTAFSGSHQDAIKKGFDARRP----- 351
                                             *************************************************************98643..... PP

                               TIGR00970 356 dtlwkvpylpldpkdvgreyeavirvnsqsGkGGvayvlktdlGldlprrlqiefssvvkdiadskGkels 426
                                                w++pylp+dp+d+g  yeavirvnsqsGk G a+++ +++Gl+lpr+lq +fs  v+  +d++Gke++
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 352 GDRWEMPYLPIDPQDIGCSYEAVIRVNSQSGKSGSAWLIEQNHGLKLPRALQQDFSLHVQRETDTHGKEMT 422
                                             346******************************************************************** PP

                               TIGR00970 427 skeisdlfkeeyllnveqlerislvdyaveddGteskvitavvkikgekkdieGsGnGplsalvdaladll 497
                                              + +++lf+  y l  +    + l dy+ +++  ++ +++a ++i ge++ ++  GnG lsa    l+ ll
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 423 HNALWQLFRARYGLVPQ--PPLALLDYQSDSQQDGQLSLQASLRIAGETRRLQSRGNGLLSAAASGLSGLL 491
                                             ************99544..45677788888888789*********************************** PP

                               TIGR00970 498 nvdvavadysehalgsGddakaasyvelsvrrasdaekatvwGvGiaedvtsaslravlsavn 560
                                             + ++ + dy eh+lg  +d+++ +y++ ++ +         wGvGi++dv+ asl+a+  a++
  lcl|FitnessBrowser__Koxy:BWI76_RS22105 492 KQNIVIKDYHEHTLGERSDSRSVAYIRCVFPNGD-----SRWGVGIDNDVARASLQALCNAMS 549
                                             ******************************8876.....69****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (564 nodes)
Target sequences:                          1  (558 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.95
//
[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