Alignments for a candidate for leuC in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate HSERO_RS16515 HSERO_RS16515 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__HerbieS:HSERO_RS16515
          Length = 466

 Score =  592 bits (1527), Expect = e-174
 Identities = 290/466 (62%), Positives = 356/466 (76%), Gaps = 1/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M KTLY+KL+++HVV+  ++ T +LYIDRHL+HEVTSPQAF+GL+  GR   +       
Sbjct: 1   MLKTLYDKLWESHVVHTEDDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNSANLMV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +       ++R+Q++ L  N KE+ +  + +N   QGIVHV+GPEQG TLP
Sbjct: 61  ADHNVPTTDRAHGIADPISRLQVETLDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMT+VCGDSHT+THGAF ALA GIGTSEVEHVLATQTL   ++K M ++V G    G+TA
Sbjct: 121 GMTVVCGDSHTSTHGAFAALAHGIGTSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLA+IGK G+AGGTG+ +EF G  IR LSMEGRMT+CNMAIE GA+AG+VA D+TT 
Sbjct: 181 KDIVLAVIGKIGTAGGTGYAIEFAGSTIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTL 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
            Y+KGR  +P G  ++ AV+YW++L +D GA FD VVTL A EI PQVTWGT+P  V++V
Sbjct: 241 EYLKGRPFSPSGPHWERAVSYWRSLHSDPGAKFDMVVTLNAAEIKPQVTWGTSPEMVVAV 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  +PDP    DP +R   EKALAYM LKP  P+ ++ IDKVFIGSCTNSRIEDLR AA+
Sbjct: 301 DARVPDPDKEKDPTKRDGMEKALAYMALKPNTPIEDIRIDKVFIGSCTNSRIEDLREAAK 360

Query: 361 IAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           + +G+  A  V+ A+VVPGSG VK QAE EGLDKIF +AGFEWR PGCSMCLAMN DRL 
Sbjct: 361 VVRGKFRASNVKLAMVVPGSGLVKEQAEREGLDKIFRDAGFEWREPGCSMCLAMNADRLE 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAA + GHF D+R++
Sbjct: 421 PGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAGIAGHFVDVRSL 466


Lambda     K      H
   0.317    0.134    0.396 

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: 729
Number of extensions: 26
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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: 51 (24.3 bits)

Align candidate HSERO_RS16515 HSERO_RS16515 (isopropylmalate isomerase)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.19088.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.7e-240  782.9   0.0   5.3e-240  782.7   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS16515  HSERO_RS16515 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS16515  HSERO_RS16515 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  782.7   0.0  5.3e-240  5.3e-240       1     465 [.       1     465 [.       1     466 [] 1.00

  Alignments for each domain:
  == domain 1  score: 782.7 bits;  conditional E-value: 5.3e-240
                                  TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste 68 
                                                m ktly+kl+++hvv+ ++++t +lyidrhl+hevtspqafegl+ agr+  r +  l   dhn++t+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515   1 MLKTLYDKLWESHVVHTEDDGTAILYIDRHLLHEVTSPQAFEGLKLAGRQPWRNSANLMVADHNVPTT 68 
                                                679***************************************************************** PP

                                  TIGR00170  69 srdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathga 136
                                                 r   i +  ++lqv++l+ n+ke+ + +f++++++qgivhv+gpe+g tlpg+t+vcgdsht+thga
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515  69 DRAHGIADPISRLQVETLDGNAKEYSLTYFGMNDKRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGA 136
                                                ******************************************************************** PP

                                  TIGR00170 137 fgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefa 204
                                                f ala gigtsevehvlatqtl   ++k++ ++v+g l  g+takdi+la+igkig+aggtgy +efa
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515 137 FAALAHGIGTSEVEHVLATQTLLARKSKAMLVQVDGALPAGVTAKDIVLAVIGKIGTAGGTGYAIEFA 204
                                                ******************************************************************** PP

                                  TIGR00170 205 geairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272
                                                g +ir+lsme+rmtvcnmaieaga+ag++a d+tt+ey+k+r+++p g ++e av+yw++l++d+gak
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515 205 GSTIRSLSMEGRMTVCNMAIEAGARAGMVAFDDTTLEYLKGRPFSPSGPHWERAVSYWRSLHSDPGAK 272
                                                ******************************************************************** PP

                                  TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvd 340
                                                fd vvtl+a +i pqvtwgt+p++v++v+  vpdp++  dp ++ ++ekalay+ l+p+t+++di++d
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515 273 FDMVVTLNAAEIKPQVTWGTSPEMVVAVDARVPDPDKEKDPTKRDGMEKALAYMALKPNTPIEDIRID 340
                                                ******************************************************************** PP

                                  TIGR00170 341 kvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagc 408
                                                kvfigsctnsriedlr+aa+vv+gk  a+nvkla+vvpgsglvk+qae+egldkif +agfewre+gc
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515 341 KVFIGSCTNSRIEDLREAAKVVRGKFRASNVKLAMVVPGSGLVKEQAEREGLDKIFRDAGFEWREPGC 408
                                                ******************************************************************** PP

                                  TIGR00170 409 slclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                                s+cl+mn d+l+++ercastsnrnfegrqg+g+rthlvspamaaaa++ag+fvd+r 
  lcl|FitnessBrowser__HerbieS:HSERO_RS16515 409 SMCLAMNADRLEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAGIAGHFVDVRS 465
                                                *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.20
//
[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