Alignments for a candidate for leuA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Dyella japonica UNC79MFTsu3.2

Align 2-isopropylmalate synthase 1; Alpha-IPM synthase 1; Alpha-isopropylmalate synthase 1; EC 2.3.3.13 (characterized)
to candidate N515DRAFT_0574 N515DRAFT_0574 2-isopropylmalate synthase

Query= SwissProt::Q8F445
         (501 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0574
          Length = 535

 Score =  469 bits (1206), Expect = e-136
 Identities = 240/498 (48%), Positives = 334/498 (67%), Gaps = 2/498 (0%)

Query: 5   DYVRIFDTTLRDGEQCPGAAMTENEKLEIASQLATMKVDIIEAGFPVSSPVQFQAVERIA 64
           D VRIFDTTLRDGEQ PG  M    KL +A  L  + VD++EAGFP +SP  F AV  IA
Sbjct: 20  DRVRIFDTTLRDGEQAPGFGMDRRAKLRMAHALEALGVDVMEAGFPQASPDDFAAVADIA 79

Query: 65  RETEGPMIAALARAMKADIEAASKALQPAKKRRIHTFIASSPIHMKYKLGKEPKEVLKMA 124
           +      + ALAR   ADI+ A +AL+ A+  RIH F+++SP+H ++KLG   ++V+  A
Sbjct: 80  KAVRHSTVCALARCQAADIDTAGRALEAAQHSRIHVFLSTSPLHREHKLGMSKQQVIDTA 139

Query: 125 VEAVTLCRQFVDDVEFSPEDATRSEPEFLRELCEAVIAAGATTINIPDTVGYTTPAEYGG 184
           + AV   R    +VEFS EDA R+EP++L E+  A IAAGATT+N PDTVGY TPAE   
Sbjct: 140 IAAVERARALCHEVEFSAEDAMRTEPDYLAEVFSAAIAAGATTVNAPDTVGYVTPAEIAE 199

Query: 185 LFKFLLSNVRGAEKIIFSAHCHNDLGLATANSLAAVQNGARQIECTINGIGERAGNTAME 244
            F +L  +V+GAE+++FS+HCH+DLG+A ANSLAAV  GARQIECTINGIGERAGN ++E
Sbjct: 200 RFAYLRKHVKGAERVVFSSHCHDDLGMAVANSLAAVSAGARQIECTINGIGERAGNASLE 259

Query: 245 EVVMAMRTRKDTFGIQTQIKTEEIARASYLVKTITGMLVQPNKAIVGANAFAHESGIHQD 304
           EVVMA+R R   FG+ ++I    + + S L+  +TG  V  NKAIVG NAFAHESGIHQ 
Sbjct: 260 EVVMALRVRGPYFGVDSRIDARRLVQTSRLLTQLTGQAVPRNKAIVGDNAFAHESGIHQH 319

Query: 305 GVIKHRETYEIMKPETVGLSSNRMVLGRHSGRAGFKDRIVKLGFSPQVEELEAAYQRFLE 364
           G++KHR TYEIM+P+ VG+   ++VLG+HSGR   + R+  LG +P+   ++  + RF  
Sbjct: 320 GMLKHRGTYEIMRPQDVGMGETKLVLGKHSGRHALRSRLQALGHTPEEAAMDDIFARFKA 379

Query: 365 IADRKKEIYDEDIRALFSEEARKSTGDRFQLEGFTVSTGTKSTPTAGVRIL-IDGHVREE 423
           +AD+K+EI+DED+ AL   +   + G  +++     S+    + +A VR+   DG    E
Sbjct: 380 LADKKREIHDEDLEALALGQDPDAAGP-WRIVQLNSSSHLGGSASASVRLAHDDGREIGE 438

Query: 424 SATGDGPVDAIYKAIQKTTGMDPEVSRLVISPVTEGQDAMAEASVTLEYKGDRVVGKGSS 483
           +A GDGPVDA+ +A+++ TG D E+++  +  V+EG DA  +A +T  +      G G S
Sbjct: 439 AAIGDGPVDAVLRAMERATGTDLELTQFQVRAVSEGGDAQGQAQLTARHAARNWRGNGVS 498

Query: 484 TDIIEACSRAYISALNRL 501
           TDI+EA + A +S +NR+
Sbjct: 499 TDIVEATALAALSIVNRI 516


Lambda     K      H
   0.316    0.132    0.364 

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: 651
Number of extensions: 24
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: 501
Length of database: 535
Length adjustment: 35
Effective length of query: 466
Effective length of database: 500
Effective search space:   233000
Effective search space used:   233000
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: 52 (24.6 bits)

Align candidate N515DRAFT_0574 N515DRAFT_0574 (2-isopropylmalate synthase)
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.30692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-200  653.2   1.4   1.2e-200  653.0   1.4    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574  N515DRAFT_0574 2-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0574  N515DRAFT_0574 2-isopropylmalate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.0   1.4  1.2e-200  1.2e-200       1     494 []      21     514 ..      21     514 .. 0.99

  Alignments for each domain:
  == domain 1  score: 653.0 bits;  conditional E-value: 1.2e-200
                                    TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknar 66 
                                                  rv ifdttlrdGeqapg+ +  + kl++a+ale lgvd++eaGfp +s+ df av  ia++v++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574  21 RVRIFDTTLRDGEQAPGFGMDRRAKLRMAHALEALGVDVMEAGFPQASPDDFAAVADIAKAVRHST 86 
                                                  799*************************************************************** PP

                                    TIGR00973  67 vvglaravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvdd 132
                                                  v++lar+   did a +al+ a++ rih+f++ts++h+e+kl ++k++v++ +++av++a+ + ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574  87 VCALARCQAADIDTAGRALEAAQHSRIHVFLSTSPLHREHKLGMSKQQVIDTAIAAVERARALCHE 152
                                                  ****************************************************************** PP

                                    TIGR00973 133 vefsaedagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsv 198
                                                  vefsaeda rte ++la+v+ aai aGatt+n PdtvGy++Pae +e +++l+++v + +++++s 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 153 VEFSAEDAMRTEPDYLAEVFSAAIAAGATTVNAPDTVGYVTPAEIAERFAYLRKHVKGAERVVFSS 218
                                                  ****************************************************************** PP

                                    TIGR00973 199 hchddlGlavanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiy 264
                                                  hchddlG+avanslaav +Garq+ectinGiGeraGna+leevvmal+vr  +++v+  i+ +++ 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 219 HCHDDLGMAVANSLAAVSAGARQIECTINGIGERAGNASLEEVVMALRVRGPYFGVDSRIDARRLV 284
                                                  ****************************************************************** PP

                                    TIGR00973 265 rtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsG 330
                                                  +tsrl+++ltg +v+rnkaivGdnafahesGihq+G+lk++ tyei++p+++G+ ++klvlgk+sG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 285 QTSRLLTQLTGQAVPRNKAIVGDNAFAHESGIHQHGMLKHRGTYEIMRPQDVGMGETKLVLGKHSG 350
                                                  ****************************************************************** PP

                                    TIGR00973 331 raalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvq 396
                                                  r+al++rl++lG+  +e  +d +f +fk ladkk+e++dedleal+l +   +    +++++l+ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 351 RHALRSRLQALGHTPEEAAMDDIFARFKALADKKREIHDEDLEALALGQDP-DAAGPWRIVQLNSS 415
                                                  **********************************************98776.78888********* PP

                                    TIGR00973 397 sgeesvptatvklkvk.geekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgev 461
                                                  s     + a v+l+ + g e  +aa+G Gpvdav++a+e++++++ +l++++++a++eg da+g++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 416 SHLGGSASASVRLAHDdGREIGEAAIGDGPVDAVLRAMERATGTDLELTQFQVRAVSEGGDAQGQA 481
                                                  99999*********997889********************************************** PP

                                    TIGR00973 462 kvvlelngkkysGrgvatdiveasakayvnaln 494
                                                  ++++++ +++  G gv+tdivea+a a + ++n
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0574 482 QLTARHAARNWRGNGVSTDIVEATALAALSIVN 514
                                                  ****************************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (535 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.85
//
[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