Alignments for a candidate for leuA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Shewanella amazonensis SB2B

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate 6936138 Sama_0335 2-isopropylmalate synthase (RefSeq)

Query= SwissProt::P15875
         (523 letters)



>FitnessBrowser__SB2B:6936138
          Length = 522

 Score =  692 bits (1786), Expect = 0.0
 Identities = 350/518 (67%), Positives = 420/518 (81%), Gaps = 1/518 (0%)

Query: 1   MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60
           MS +VIIFDTTLRDGEQAL ASLS KEKLQ+ALALER+GVDVMEVGFPVSSPGDFESVQT
Sbjct: 1   MSDRVIIFDTTLRDGEQALAASLSVKEKLQVALALERLGVDVMEVGFPVSSPGDFESVQT 60

Query: 61  IARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSPMHIATKLRSTLDEVIE 120
           IAR IKNSRVCAL+R +EKDID AAQAL VA+ FRIHTFI+TS +H+ +KL+ + D+V++
Sbjct: 61  IARHIKNSRVCALSRALEKDIDAAAQALSVAEQFRIHTFISTSNIHVESKLKRSFDQVLD 120

Query: 121 RAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGARTINIPDTVGYTMPFEF 180
            AV  VK AR +TDDVEFSCEDAGRTP+D+L R+VEAAI+AGARTINIPDTVGYT+P EF
Sbjct: 121 MAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAISAGARTINIPDTVGYTVPSEF 180

Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGARQVEGAMNGIGERAGNCA 240
            GII  L+ RVPNID+A+ISVH HDDLG++V NS+AAV AGARQ+E  +NGIGERAGNC+
Sbjct: 181 GGIIQTLFNRVPNIDQAVISVHCHDDLGLSVANSIAAVQAGARQIECTVNGIGERAGNCS 240

Query: 241 LEEVIMAIKVRKDIMNVHTNINHHEIWRTSQTVSQICNMPIPANKAIVGSGAFAHSSGIH 300
           LEE+ M +  RKD++ ++TNIN  EI RTS  VSQ+CNMPI  NKAIVGS AF HSSGIH
Sbjct: 241 LEEIAMILATRKDMLGLYTNINAREIHRTSSLVSQLCNMPIQPNKAIVGSNAFTHSSGIH 300

Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMEEMGYKDTDYNMDHLYDAF 360
           QDG+LK +  YEIMTPESIGLN+  LN+TSRSGR  +KHRMEEMGY   DY+MD LY AF
Sbjct: 301 QDGMLKAQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGAGDYDMDTLYAAF 360

Query: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSD-IATASVKLACGEEIK 419
           LKLADKKGQVFDYDLEALAF+  Q E+ +H+ ++   VQS S++  ATA+V++  G+E+ 
Sbjct: 361 LKLADKKGQVFDYDLEALAFMEAQAEDDDHYVMEQLVVQSDSTEGKATATVRMRVGDEVI 420

Query: 420 AEAANGNGPVDAIYQAINRITGYDVELVKYDLNAKGQGKDALGQVDIVVNHHGRRFHGVG 479
            EAA GNGPVDA Y AI R T   + +  Y L AKG+G++ALGQVDI   +  R FHGVG
Sbjct: 421 TEAATGNGPVDAAYNAIARATHRTINISSYKLGAKGEGQNALGQVDITARYDDRNFHGVG 480

Query: 480 LATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKE 517
           LATD+VE+SA+A+VHV+N  WRA +V    Q+  Q +E
Sbjct: 481 LATDVVEASAQALVHVMNLTWRADKVAYCKQQMQQTRE 518


Lambda     K      H
   0.317    0.132    0.372 

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: 754
Number of extensions: 31
Number of successful extensions: 2
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: 523
Length of database: 522
Length adjustment: 35
Effective length of query: 488
Effective length of database: 487
Effective search space:   237656
Effective search space used:   237656
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 6936138 Sama_0335 (2-isopropylmalate synthase (RefSeq))
to HMM TIGR00973 (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/TIGR00973.hmm
# target sequence database:        /tmp/gapView.29153.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00973  [M=494]
Accession:   TIGR00973
Description: leuA_bact: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-240  784.3   8.6   2.3e-240  784.1   8.6    1.0  1  lcl|FitnessBrowser__SB2B:6936138  Sama_0335 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6936138  Sama_0335 2-isopropylmalate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.1   8.6  2.3e-240  2.3e-240       1     494 []       4     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 784.1 bits;  conditional E-value: 2.3e-240
                         TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekd 77 
                                       rv+ifdttlrdGeqa+ asl+v+eklq+a+alerlgvd++e+Gfpvss+gdfe+vq+iar++kn+rv++l+ra+ekd
  lcl|FitnessBrowser__SB2B:6936138   4 RVIIFDTTLRDGEQALAASLSVKEKLQVALALERLGVDVMEVGFPVSSPGDFESVQTIARHIKNSRVCALSRALEKD 80 
                                       79*************************************************************************** PP

                         TIGR00973  78 idaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvvea 154
                                       idaaa+al +ae++rihtfi+ts+ih+e klk+++d+vl+++v avkya+ f+ddvefs+edagrt++++l+r+vea
  lcl|FitnessBrowser__SB2B:6936138  81 IDAAAQALSVAEQFRIHTFISTSNIHVESKLKRSFDQVLDMAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEA 157
                                       ***************************************************************************** PP

                         TIGR00973 155 aieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGe 231
                                       ai+aGa tiniPdtvGy++P+e+g +i++l ++vPnid+a++svhchddlGl+vans+aav++Garq+ect+nGiGe
  lcl|FitnessBrowser__SB2B:6936138 158 AISAGARTINIPDTVGYTVPSEFGGIIQTLFNRVPNIDQAVISVHCHDDLGLSVANSIAAVQAGARQIECTVNGIGE 234
                                       ***************************************************************************** PP

                         TIGR00973 232 raGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknkety 308
                                       raGn++lee++m+l +rkd+l+++t+in +ei+rts lvs+l++m++q+nkaivG+naf h+sGihqdG+lk ++ty
  lcl|FitnessBrowser__SB2B:6936138 235 RAGNCSLEEIAMILATRKDMLGLYTNINAREIHRTSSLVSQLCNMPIQPNKAIVGSNAFTHSSGIHQDGMLKAQNTY 311
                                       ***************************************************************************** PP

                         TIGR00973 309 eilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeee 385
                                       ei++pesiGl++++l++++rsGr+ +k+r+ee+G+   ++++d l+ +f++ladkk++vfd+dleal++ e + e++
  lcl|FitnessBrowser__SB2B:6936138 312 EIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGAGDYDMDTLYAAFLKLADKKGQVFDYDLEALAFMEAQAEDD 388
                                       ***************************************************************************** PP

                         TIGR00973 386 eklkleklqvqsge.esvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgev 461
                                       +++ +e+l vqs + e  +tatv+++v +e  ++aatGnGpvda y+ai ++++  ++++ y++ akgeg++alg+v
  lcl|FitnessBrowser__SB2B:6936138 389 DHYVMEQLVVQSDStEGKATATVRMRVGDEVITEAATGNGPVDAAYNAIARATHRTINISSYKLGAKGEGQNALGQV 465
                                       ***********97615689********9888********************************************** PP

                         TIGR00973 462 kvvlelngkkysGrgvatdiveasakayvnaln 494
                                       ++++++++++++G+g+atd+veasa+a+v+++n
  lcl|FitnessBrowser__SB2B:6936138 466 DITARYDDRNFHGVGLATDVVEASAQALVHVMN 498
                                       *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (522 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.57
//
[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