GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Azorhizobium caulinodans ORS 571

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_012172581.1 AZC_RS20820 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000010525.1:WP_012172581.1
          Length = 474

 Score =  595 bits (1535), Expect = e-175
 Identities = 295/461 (63%), Positives = 353/461 (76%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K+FD HVV   E+ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A +D
Sbjct: 9   KTLYDKIFDDHVVSRQEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPSKTLAVVD 68

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T  +        +  Q++ L +N +EFG+E Y+     QGIVHV+GPEQG TLPG 
Sbjct: 69  HNVPTTDRSHGIDDPESATQVETLAENTREFGIEYYNERDIRQGIVHVIGPEQGFTLPGT 128

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           TIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q ++K M++ V G    G+ AKD
Sbjct: 129 TIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMRVTVDGTLPEGVGAKD 188

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           + LAIIG  G+AGGTG+V+E+ G+ +R LSMEGRMT+CNM+IE GA+AG+VAPDE  F Y
Sbjct: 189 VTLAIIGSIGTAGGTGYVIEYAGDVMRQLSMEGRMTVCNMSIEGGARAGMVAPDEKAFAY 248

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           +K R  APKG D+D AVAYW+TL++DEGA FD  V L    + P V+WGT+P  V+SV  
Sbjct: 249 LKDRPRAPKGADWDKAVAYWETLRSDEGAYFDAEVRLDGANLPPIVSWGTSPEDVVSVEG 308

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +PDP +  D V R + ++ALAYMGL  G  ++++AID+VFIGSCTN RIED+R AA+I 
Sbjct: 309 LVPDPEAIEDAVRRDAKKRALAYMGLTAGTKISDIAIDRVFIGSCTNGRIEDMRQAAQIV 368

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
            G  V   V+A+VVPGSG VKAQAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL+P E
Sbjct: 369 AGHTVNANVKAMVVPGSGLVKAQAEAEGLDKIFLAAGFEWREPGCSMCLAMNADRLSPEE 428

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCASTSNRNFEGRQG  GRTHLVSPAMAAAAA+ G F D+R
Sbjct: 429 RCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAIAGRFVDVR 469


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: 759
Number of extensions: 28
Number of successful extensions: 1
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: 474
Length adjustment: 33
Effective length of query: 433
Effective length of database: 441
Effective search space:   190953
Effective search space used:   190953
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 WP_012172581.1 AZC_RS20820 (3-isopropylmalate dehydratase large subunit)
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.1932382.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.7e-245  799.7   0.3   4.2e-245  799.5   0.3    1.0  1  NCBI__GCF_000010525.1:WP_012172581.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000010525.1:WP_012172581.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  799.5   0.3  4.2e-245  4.2e-245       2     465 ..       8     470 ..       7     471 .. 1.00

  Alignments for each domain:
  == domain 1  score: 799.5 bits;  conditional E-value: 4.2e-245
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 
                                           +ktly+k+fd hvv ++e++t llyidrhlvhevtspqafeglr agrkvr ++ktla +dhn++t+ r   i
  NCBI__GCF_000010525.1:WP_012172581.1   8 PKTLYDKIFDDHVVSRQEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPSKTLAVVDHNVPTTDRSHGI 80 
                                           8************************************************************************ PP

                             TIGR00170  75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                            + ++  qv++l +n++efg+++++ ++ +qgivhv+gpe+g+tlpg+tivcgdsht+thgafgala gigts
  NCBI__GCF_000010525.1:WP_012172581.1  81 DDPESATQVETLAENTREFGIEYYNERDIRQGIVHVIGPEQGFTLPGTTIVCGDSHTSTHGAFGALAHGIGTS 153
                                           ************************************************************************* PP

                             TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220
                                           evehvlatqtl+q+++k+++++v+g+l +g+ akd+ laiig ig+aggtgyv+e+ag+++r+lsme+rmtvc
  NCBI__GCF_000010525.1:WP_012172581.1 154 EVEHVLATQTLIQKKSKNMRVTVDGTLPEGVGAKDVTLAIIGSIGTAGGTGYVIEYAGDVMRQLSMEGRMTVC 226
                                           ************************************************************************* PP

                             TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293
                                           nm+ie ga+ag++apde +f+y+kdr+ apkg++++kavayw tl++dega fd +v l++ ++ p v+wgt+
  NCBI__GCF_000010525.1:WP_012172581.1 227 NMSIEGGARAGMVAPDEKAFAYLKDRPRAPKGADWDKAVAYWETLRSDEGAYFDAEVRLDGANLPPIVSWGTS 299
                                           ************************************************************************* PP

                             TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366
                                           p++v+sv++ vpdp+ + d v++   ++alay+gl++gtk+ di++d+vfigsctn+ried+r+aa++v g+ 
  NCBI__GCF_000010525.1:WP_012172581.1 300 PEDVVSVEGLVPDPEAIEDAVRRDAKKRALAYMGLTAGTKISDIAIDRVFIGSCTNGRIEDMRQAAQIVAGHT 372
                                           ************************************************************************* PP

                             TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439
                                           v  nvk a+vvpgsglvk+qae+egldkifl+agfewre+gcs+cl+mn d+l++ ercastsnrnfegrqg 
  NCBI__GCF_000010525.1:WP_012172581.1 373 VNANVK-AMVVPGSGLVKAQAEAEGLDKIFLAAGFEWREPGCSMCLAMNADRLSPEERCASTSNRNFEGRQGF 444
                                           ******.****************************************************************** PP

                             TIGR00170 440 garthlvspamaaaaavagkfvdire 465
                                           ++rthlvspamaaaaa+ag+fvd+r 
  NCBI__GCF_000010525.1:WP_012172581.1 445 KGRTHLVSPAMAAAAAIAGRFVDVRT 470
                                           ************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (474 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: 16.74
//
[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:

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:

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:

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:

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