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

GapMind for Amino acid biosynthesis

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

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate 5211056 Shew_3472 2-isopropylmalate synthase (RefSeq)

Query= SwissProt::P15875
         (523 letters)



>FitnessBrowser__PV4:5211056
          Length = 523

 Score =  683 bits (1762), Expect = 0.0
 Identities = 345/522 (66%), Positives = 416/522 (79%), Gaps = 8/522 (1%)

Query: 1   MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQT 60
           MS +VIIFDTTLRDGEQAL ASL+ KEKLQIAL+LER+GVDVMEVGFPVSSPGDFESVQT
Sbjct: 1   MSNRVIIFDTTLRDGEQALAASLTVKEKLQIALSLERLGVDVMEVGFPVSSPGDFESVQT 60

Query: 61  IARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSPMHIATKLRSTLDEVIE 120
           IARTIKNSRVCALAR +EKDID AAQ+L VA+ FRIHTFI+TS +H+ +KL+ + D+V++
Sbjct: 61  IARTIKNSRVCALARALEKDIDAAAQSLSVAEQFRIHTFISTSTIHVESKLKRSFDQVLD 120

Query: 121 RAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGARTINIPDTVGYTMPFEF 180
            AV  VK AR +TDDVEFSCEDAGRTP+D+L R+VEAAI AGA+TINIPDTVGYT+P EF
Sbjct: 121 MAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAIKAGAKTINIPDTVGYTVPSEF 180

Query: 181 AGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGARQVEGAMNGIGERAGNCA 240
            GII  L++RVPNID+A+ISVH HDDLG++V NS+ AV  GARQ+E  +NGIGERAGNC+
Sbjct: 181 GGIIQNLFDRVPNIDQAVISVHCHDDLGLSVANSITAVQHGARQIECTVNGIGERAGNCS 240

Query: 241 LEEVIMAIKVRKDIMNVHTNINHHEIWRTSQTVSQICNMPIPANKAIVGSGAFAHSSGIH 300
           LEE+ M I  RK  + + T IN  EI RTS  VSQ+CNMP+ ANKAIVG+ AF HSSGIH
Sbjct: 241 LEEIAMIIATRKASLGLETGINAKEIHRTSNLVSQLCNMPVQANKAIVGANAFTHSSGIH 300

Query: 301 QDGVLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMEEMGYKDTDYNMDHLYDAF 360
           QDGVLK++  YEIMTPESIGLN+  LN+TSRSGR  +KHRMEEMGY + DY+MD LY+AF
Sbjct: 301 QDGVLKSQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGEQDYDMDTLYEAF 360

Query: 361 LKLADKKGQVFDYDLEALAFINKQQEEPEHFRLDYFSVQSGSSD-IATASVKLACGEEIK 419
           LKLADKKGQVFDYDLEAL ++  Q E+  H+ L    V S S+   ATA+V L+   +  
Sbjct: 361 LKLADKKGQVFDYDLEALVYVEAQAEDENHYGLQQLVVHSDSTQGQATATVTLSIDGKAV 420

Query: 420 AEAANGNGPVDAIYQAINRITGYDVELVKYDLNAKGQGKDALGQVDIVVNHHGRRFHGVG 479
            EAA GNGPVDA Y+AI R +G ++ +  Y L+AKGQG+DALGQVDI   +H + FHGVG
Sbjct: 421 TEAATGNGPVDAAYKAIARASGCEINISSYQLSAKGQGQDALGQVDITAKYHDQSFHGVG 480

Query: 480 LATDIVESSAKAMVHVLNNIWRAAEVEKELQRKAQNKENNKE 521
           LATD+VE+SA A++HV+N  WRA +V       A+NK   K+
Sbjct: 481 LATDVVEASAAALIHVMNLTWRADKV-------AENKHKLKQ 515


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: 764
Number of extensions: 28
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: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
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 5211056 Shew_3472 (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.32480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.4e-241  788.1  10.7   1.6e-241  787.9  10.7    1.0  1  lcl|FitnessBrowser__PV4:5211056  Shew_3472 2-isopropylmalate synt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5211056  Shew_3472 2-isopropylmalate synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  787.9  10.7  1.6e-241  1.6e-241       1     494 []       4     498 ..       4     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 787.9 bits;  conditional E-value: 1.6e-241
                        TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravekdi 78 
                                      rv+ifdttlrdGeqa+ asltv+eklqia+ lerlgvd++e+Gfpvss+gdfe+vq+iar++kn+rv++lara+ekdi
  lcl|FitnessBrowser__PV4:5211056   4 RVIIFDTTLRDGEQALAASLTVKEKLQIALSLERLGVDVMEVGFPVSSPGDFESVQTIARTIKNSRVCALARALEKDI 81 
                                      79**************************************************************************** PP

                        TIGR00973  79 daaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvveaai 156
                                      daaa++l +ae++rihtfi+ts ih+e klk+++d+vl+++v avkya+ f+ddvefs+edagrt++++l+r+veaai
  lcl|FitnessBrowser__PV4:5211056  82 DAAAQSLSVAEQFRIHTFISTSTIHVESKLKRSFDQVLDMAVGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAI 159
                                      ****************************************************************************** PP

                        TIGR00973 157 eaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinGiGeraG 234
                                      +aGa tiniPdtvGy++P+e+g +i++l ++vPnid+a++svhchddlGl+vans++av++Garq+ect+nGiGeraG
  lcl|FitnessBrowser__PV4:5211056 160 KAGAKTINIPDTVGYTVPSEFGGIIQNLFDRVPNIDQAVISVHCHDDLGLSVANSITAVQHGARQIECTVNGIGERAG 237
                                      ****************************************************************************** PP

                        TIGR00973 235 naaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeils 312
                                      n++lee++m++ +rk  l++etgin kei+rts+lvs+l++m+vq+nkaivG+naf h+sGihqdGvlk ++tyei++
  lcl|FitnessBrowser__PV4:5211056 238 NCSLEEIAMIIATRKASLGLETGINAKEIHRTSNLVSQLCNMPVQANKAIVGANAFTHSSGIHQDGVLKSQNTYEIMT 315
                                      ****************************************************************************** PP

                        TIGR00973 313 pesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkl 390
                                      pesiGl++++l++++rsGr+ +k+r+ee+G+ ++++++d l+e+f++ladkk++vfd+dlealv+ e + e+e+++ l
  lcl|FitnessBrowser__PV4:5211056 316 PESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGEQDYDMDTLYEAFLKLADKKGQVFDYDLEALVYVEAQAEDENHYGL 393
                                      ****************************************************************************** PP

                        TIGR00973 391 eklqvqsgees.vptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlel 467
                                      ++l v+s +++  +tatv+l ++g+  ++aatGnGpvda ykai ++ + e++++ y++ akg+g+dalg+v++++++
  lcl|FitnessBrowser__PV4:5211056 394 QQLVVHSDSTQgQATATVTLSIDGKAVTEAATGNGPVDAAYKAIARASGCEINISSYQLSAKGQGQDALGQVDITAKY 471
                                      ******98765389**************************************************************** PP

                        TIGR00973 468 ngkkysGrgvatdiveasakayvnaln 494
                                      +++ ++G+g+atd+veasa a+++++n
  lcl|FitnessBrowser__PV4:5211056 472 HDQSFHGVGLATDVVEASAAALIHVMN 498
                                      *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (523 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: 00:00:00.02
# Mc/sec: 9.88
//
[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