Alignments for a candidate for leuA in Desulforamulus ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulforamulus ruminis DSM 2154

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_013840144.1 DESRU_RS00330 2-isopropylmalate synthase

Query= reanno::Btheta:351389
         (498 letters)



>NCBI__GCF_000215085.1:WP_013840144.1
          Length = 501

 Score =  489 bits (1259), Expect = e-143
 Identities = 252/497 (50%), Positives = 351/497 (70%), Gaps = 2/497 (0%)

Query: 4   RLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIEISK 63
           +L+IFDTTLRDGEQ  G  LNT EK+++A+ L  LGVDVIEAGFP SSPGD NSV  I++
Sbjct: 3   KLYIFDTTLRDGEQSLGITLNTHEKLEIARQLVRLGVDVIEAGFPASSPGDMNSVKTIAR 62

Query: 64  AVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIERAV 123
            +    IC LTRAV KDID   +AL+ A+  RIHTGI  S  H++ K   + E+++E AV
Sbjct: 63  EIKGAVICGLTRAVAKDIDACAEALRDAEQPRIHTGIAVSPVHMEKKLRLSPEQVVEAAV 122

Query: 124 AAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEYGAK 183
           AAVK+A+++V DVEFYAEDA R++  +LA+++E VI+AGATVVNIPDT GY  P +YG  
Sbjct: 123 AAVKHAKKYVSDVEFYAEDASRSEPAFLAKILEKVIEAGATVVNIPDTVGYVTPWQYGEL 182

Query: 184 IKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTALEE 243
           I +L  +V  ID+AI+STHCHNDLGMATANT+A V  GA QVE TINGIGERAGNTALEE
Sbjct: 183 ISFLTKNVKNIDSAIISTHCHNDLGMATANTLAAVKAGASQVEGTINGIGERAGNTALEE 242

Query: 244 IAMIIKSHHEI-DIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQDG 302
           + M + S   +  ++  + T++I  TSR+VS +  +PV  +KAIVG NAF H+SGIHQDG
Sbjct: 243 VMMAVYSQPSLYGVELGVKTKEIAATSRLVSGITGVPVPSHKAIVGANAFMHASGIHQDG 302

Query: 303 VLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFLKL 362
           VLK   TYEIIDP  VGI  N IVL+ARSGR ALK+RL  LG + +Q  ++ VY+EFL+L
Sbjct: 303 VLKEKRTYEIIDPETVGILRNKIVLSARSGRHALKHRLEELGYSPEQYDVETVYKEFLQL 362

Query: 363 ADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACASG 422
           AD+KK++ D+D+  L G    + + I ++ + V +     + A++ L ++ +     A G
Sbjct: 363 ADQKKEVFDEDLHALMGYTEKERNSISIKNISVATNGAATATATVSLAMNDQILTDAAYG 422

Query: 423 NGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEY-DNQIYYGFGANTDI 481
           NGPVDA  KA+++I    + L+++ + ++S+GS+ +G   ++V Y ++ +  G G + D+
Sbjct: 423 NGPVDAVFKAIERITGITVKLEDYNLSSVSRGSEALGNAIVKVRYGESGLVIGRGVSPDV 482

Query: 482 IAASVEAYIDCINKFKA 498
           I A+ +AY++ ++K KA
Sbjct: 483 IEATAKAYVNALSKIKA 499


Lambda     K      H
   0.317    0.134    0.377 

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: 633
Number of extensions: 27
Number of successful extensions: 3
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: 498
Length of database: 501
Length adjustment: 34
Effective length of query: 464
Effective length of database: 467
Effective search space:   216688
Effective search space used:   216688
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 WP_013840144.1 DESRU_RS00330 (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.2834825.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-211  687.4   7.7   5.6e-211  687.2   7.7    1.0  1  NCBI__GCF_000215085.1:WP_013840144.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840144.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.2   7.7  5.6e-211  5.6e-211       1     493 [.       3     494 ..       3     495 .. 0.98

  Alignments for each domain:
  == domain 1  score: 687.2 bits;  conditional E-value: 5.6e-211
                             TIGR00973   1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 
                                           +++ifdttlrdGeq++g++l+++ekl+ia++l rlgvd+ieaGfp+ss+gd+++v++iare+k a+++gl+ra
  NCBI__GCF_000215085.1:WP_013840144.1   3 KLYIFDTTLRDGEQSLGITLNTHEKLEIARQLVRLGVDVIEAGFPASSPGDMNSVKTIAREIKGAVICGLTRA 75 
                                           689********************************************************************** PP

                             TIGR00973  74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146
                                           v kdida aeal++ae+ riht ia s++h+e+kl+ + ++v+e +v+avk+ak++v dvef aeda+r+e +
  NCBI__GCF_000215085.1:WP_013840144.1  76 VAKDIDACAEALRDAEQPRIHTGIAVSPVHMEKKLRLSPEQVVEAAVAAVKHAKKYVSDVEFYAEDASRSEPA 148
                                           ************************************************************************* PP

                             TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219
                                           fla+++e++ieaGat++niPdtvGy++P +ygeli+ l++nv nid ai+s hch+dlG+a+an+laavk+Ga
  NCBI__GCF_000215085.1:WP_013840144.1 149 FLAKILEKVIEAGATVVNIPDTVGYVTPWQYGELISFLTKNVKNIDSAIISTHCHNDLGMATANTLAAVKAGA 221
                                           ************************************************************************* PP

                             TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292
                                           +qve+tinGiGeraGn+aleev+ma+  + ++++ve+g++tkei +tsrlvs +tg++v++ kaivG+naf+h
  NCBI__GCF_000215085.1:WP_013840144.1 222 SQVEGTINGIGERAGNTALEEVMMAVYSQPSLYGVELGVKTKEIAATSRLVSGITGVPVPSHKAIVGANAFMH 294
                                           ************************************************************************* PP

                             TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365
                                            sGihqdGvlk+k+tyei++pe++G+ ++k+vl++rsGr+alk+rleelG+  ++++++ ++++f++lad+kk
  NCBI__GCF_000215085.1:WP_013840144.1 295 ASGIHQDGVLKEKRTYEIIDPETVGILRNKIVLSARSGRHALKHRLEELGYSPEQYDVETVYKEFLQLADQKK 367
                                           ************************************************************************* PP

                             TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438
                                           evfdedl+al+    +  e++++ +++++v +     +tatv+l+++++  ++aa GnGpvdav+kaie+i++
  NCBI__GCF_000215085.1:WP_013840144.1 368 EVFDEDLHALMGYTEK--ERNSISIKNISVATNGAATATATVSLAMNDQILTDAAYGNGPVDAVFKAIERITG 438
                                           *********9865544..667799**********************8888*********************** PP

                             TIGR00973 439 levklleysitakgegkdalgevkvvlelngk.kysGrgvatdiveasakayvnal 493
                                           + vkl++y++ ++++g++alg++ v++++ +   + Grgv+ d++ea+akayvnal
  NCBI__GCF_000215085.1:WP_013840144.1 439 ITVKLEDYNLSSVSRGSEALGNAIVKVRYGESgLVIGRGVSPDVIEATAKAYVNAL 494
                                           ****************************96542789******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (494 nodes)
Target sequences:                          1  (501 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.48
//
[ok]

This GapMind analysis is from Jul 25 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