Alignments for a candidate for leuA in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Salinicoccus carnicancri Crm

Align 2-isopropylmalate synthase 1; Alpha-IPM synthase 1; Alpha-isopropylmalate synthase 1; EC 2.3.3.13 (characterized)
to candidate WP_017548412.1 C792_RS0105305 2-isopropylmalate synthase

Query= SwissProt::Q8F445
         (501 letters)



>NCBI__GCF_000330705.1:WP_017548412.1
          Length = 515

 Score =  474 bits (1221), Expect = e-138
 Identities = 244/496 (49%), Positives = 339/496 (68%), Gaps = 2/496 (0%)

Query: 7   VRIFDTTLRDGEQCPGAAMTENEKLEIASQLATMKVDIIEAGFPVSSPVQFQAVERIARE 66
           +RIFDTTLRDGEQ PG  + + EKLEIA QL  + VD++EAGFP +S   FQAV  IA  
Sbjct: 4   IRIFDTTLRDGEQSPGVNLNKMEKLEIAKQLEKLGVDVMEAGFPAASEGDFQAVRLIADT 63

Query: 67  TEGPMIAALARAMKADIEAASKALQPAKKRRIHTFIASSPIHMKYKLGKEPKEVLKMAVE 126
                + ALAR  K DI+ A +AL+     RIH F+A+SPIHM+YKL   P+EV+K +V+
Sbjct: 64  VTDVSVTALARTRKEDIDRAWEALKNTPNPRIHIFLATSPIHMEYKLKMTPEEVIKQSVD 123

Query: 127 AVTLCRQFVDDVEFSPEDATRSEPEFLRELCEAVIAAGATTINIPDTVGYTTPAEYGGLF 186
            V   R+   +VE+S EDATRS+ +F+  + E VI  GAT IN+PDTVGYTTP EYG +F
Sbjct: 124 MVRYARERFSEVEWSAEDATRSDWDFMANIIEQVIDVGATVINLPDTVGYTTPDEYGRMF 183

Query: 187 KFLLSNVRGAEKIIFSAHCHNDLGLATANSLAAVQNGARQIECTINGIGERAGNTAMEEV 246
           K++  NV    K   S HCHNDLGLA AN++AA++NGA Q+E TINGIGERAGN A+EEV
Sbjct: 184 KYMKENVPNIAKADLSCHCHNDLGLAAANTMAAIENGATQVEGTINGIGERAGNVALEEV 243

Query: 247 VMAMRTRKDTFGIQTQIKTEEIARASYLVKTITGMLVQPNKAIVGANAFAHESGIHQDGV 306
            +A+  R D +  +T +K +EI R S L+  ++GM VQ NKAI+G NA+AHESGIHQDGV
Sbjct: 244 AVALHIRADRYNYETGLKLDEIKRTSDLIAKLSGMYVQANKAIIGRNAYAHESGIHQDGV 303

Query: 307 IKHRETYEIMKPETVGLSSNRMVLGRHSGRAGFKDRIVKLGFSPQVEELEAAYQRFLEIA 366
           +K+ ETYEI+ PE VG+SSN + +G+HSG+  FKD++ + G     EE+++ ++RF E+ 
Sbjct: 304 LKNAETYEIITPELVGVSSNTLFMGKHSGKHAFKDKVKEFGVEMTDEEVKSTFRRFKELT 363

Query: 367 DRKKEIYDEDIRALFSE-EARKSTGDRFQLEGFTVSTGTKSTPTAGVRILID-GHVREES 424
           D K+E+ D+DI  L  E +   S  +++ LE F V+ GT +  TA V +    G   + +
Sbjct: 364 DHKREVTDDDIYTLIMETKTAHSAVNKYSLENFQVNYGTANITTATVSLSTPAGRTVQTA 423

Query: 425 ATGDGPVDAIYKAIQKTTGMDPEVSRLVISPVTEGQDAMAEASVTLEYKGDRVVGKGSST 484
           ATG+G V+A+YK IQ+    + ++    ++ V  G+DA+AE+ V L   G+R  G+G++ 
Sbjct: 424 ATGNGSVEALYKTIQELIDAELKLLDYQLNSVGGGKDALAESHVQLLVNGERTNGRGTAQ 483

Query: 485 DIIEACSRAYISALNR 500
           D+IEA + AYI+A+NR
Sbjct: 484 DVIEASANAYINAVNR 499


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: 596
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: 515
Length adjustment: 34
Effective length of query: 467
Effective length of database: 481
Effective search space:   224627
Effective search space used:   224627
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 WP_017548412.1 C792_RS0105305 (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.929594.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     7e-221  719.8   8.3   7.9e-221  719.7   8.3    1.0  1  NCBI__GCF_000330705.1:WP_017548412.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017548412.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  719.7   8.3  7.9e-221  7.9e-221       1     494 []       3     498 ..       3     498 .. 0.99

  Alignments for each domain:
  == domain 1  score: 719.7 bits;  conditional E-value: 7.9e-221
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           r+ ifdttlrdGeq+pg++l+  ekl+iak+le+lgvd++eaGfp++s+gdf+av+ ia +v + +v++lar+
  NCBI__GCF_000330705.1:WP_017548412.1   3 RIRIFDTTLRDGEQSPGVNLNKMEKLEIAKQLEKLGVDVMEAGFPAASEGDFQAVRLIADTVTDVSVTALART 75 
                                           799********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                            ++did a+ealk++ + rih+f+ats+ih+e+klk+t +ev+++ v +v+ya++++ +ve+saeda+r++ +
  NCBI__GCF_000330705.1:WP_017548412.1  76 RKEDIDRAWEALKNTPNPRIHIFLATSPIHMEYKLKMTPEEVIKQSVDMVRYARERFSEVEWSAEDATRSDWD 148
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           f+a+++e++i+ Gat+in+PdtvGy++P+eyg ++k++kenvPni ka+ls hch+dlGla an++aa++nGa
  NCBI__GCF_000330705.1:WP_017548412.1 149 FMANIIEQVIDVGATVINLPDTVGYTTPDEYGRMFKYMKENVPNIAKADLSCHCHNDLGLAAANTMAAIENGA 221
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                           +qve+tinGiGeraGn+aleev++al++r d +n+etg++ +ei+rts+l++kl+gm vq+nkai+G na+ah
  NCBI__GCF_000330705.1:WP_017548412.1 222 TQVEGTINGIGERAGNVALEEVAVALHIRADRYNYETGLKLDEIKRTSDLIAKLSGMYVQANKAIIGRNAYAH 294
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                           esGihqdGvlkn etyei++pe +G+++++l +gk+sG++a+k++++e+G+++++ee++  f +fkel+d+k+
  NCBI__GCF_000330705.1:WP_017548412.1 295 ESGIHQDGVLKNAETYEIITPELVGVSSNTLFMGKHSGKHAFKDKVKEFGVEMTDEEVKSTFRRFKELTDHKR 367
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrq.eeeeklkleklqvqsgeesvptatvklkvk.geekeaaatGnGpvdavykaieki 436
                                           ev+d+d+ +l++e ++     +k+ le++qv++g+ +++tatv+l ++ g   ++aatGnG+v+a+yk+i+++
  NCBI__GCF_000330705.1:WP_017548412.1 368 EVTDDDIYTLIMETKTAhSAVNKYSLENFQVNYGTANITTATVSLSTPaGRTVQTAATGNGSVEALYKTIQEL 440
                                           ************99887477899************************967779******************** PP

                             TIGR00973 437 lelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494
                                           ++ e kll+y+++++g gkdal+e +v+l +ng++++Grg a+d++easa+ay+na+n
  NCBI__GCF_000330705.1:WP_017548412.1 441 IDAELKLLDYQLNSVGGGKDALAESHVQLLVNGERTNGRGTAQDVIEASANAYINAVN 498
                                           *********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (515 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: 00:00:00.01
# Mc/sec: 22.51
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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