GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Pontibacter ramchanderi LP43

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_101445271.1 BD749_RS13800 diaminopimelate decarboxylase

Query= reanno::Btheta:350902
         (386 letters)



>NCBI__GCF_002846395.1:WP_101445271.1
          Length = 391

 Score =  434 bits (1117), Expect = e-126
 Identities = 213/361 (59%), Positives = 273/361 (75%), Gaps = 1/361 (0%)

Query: 15  TPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTIIRESGMGADCVSGGE 74
           TPFY Y+  +LR TL   +QE A+Y ++ VHYA+KAN N  +L  +R  G GADCVSG E
Sbjct: 24  TPFYVYNLNLLRQTLQRASQEAARY-NFQVHYALKANTNSPILQEMRAVGFGADCVSGNE 82

Query: 75  IRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELEVINELAAAQNKIAN 134
           ++ A+  GFPA+ +VFAGVGK+D EIN  L+  IFCFN ES  EL V+NELA A+ K A 
Sbjct: 83  VKCAIENGFPAHHVVFAGVGKSDAEINYALDKDIFCFNCESSHELIVLNELAEAKGKTAR 142

Query: 135 VAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNVKFIGLHFHIGSQIL 194
           +A RINP+V A+TH  ITTGL ENKFGI+  ++  V+ +   + N+  IGLHFHIGSQI 
Sbjct: 143 IALRINPNVNANTHKYITTGLEENKFGINAWELPDVLALLKTLPNLSLIGLHFHIGSQIT 202

Query: 195 DMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQSVPDFKSYFATYAGQ 254
           D+  F  LC RVNE QD  E++++ +EHINVGGGLG+DY +P+ Q +PDF++YF+ +   
Sbjct: 203 DLSAFKNLCTRVNEFQDWFESQQVHLEHINVGGGLGVDYYNPDEQPIPDFEAYFSLFNQF 262

Query: 255 LKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGMTDLIRPALYQAYHK 314
           LK+RP Q +HFELGRA+V Q G+LIS+VLY+K+G    FAILDAGMT+LIRPALYQ+YHK
Sbjct: 263 LKVRPNQQVHFELGRALVAQSGTLISRVLYIKKGVSTNFAILDAGMTELIRPALYQSYHK 322

Query: 315 MENITSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSAGAYGEIMASGYNCR 374
           +ENI+S+   E YDVVGPICESSD FGKA+ L +  RGDLIA+R+AGAYGE+MAS YN R
Sbjct: 323 IENISSKGAEERYDVVGPICESSDCFGKAVVLPETNRGDLIAIRTAGAYGEVMASAYNLR 382

Query: 375 E 375
           +
Sbjct: 383 D 383


Lambda     K      H
   0.321    0.138    0.405 

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: 427
Number of extensions: 16
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: 386
Length of database: 391
Length adjustment: 30
Effective length of query: 356
Effective length of database: 361
Effective search space:   128516
Effective search space used:   128516
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_101445271.1 BD749_RS13800 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.528631.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.3e-127  410.0   0.0   4.8e-127  409.8   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101445271.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101445271.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.8   0.0  4.8e-127  4.8e-127       5     394 ..       5     389 ..       1     391 [] 0.94

  Alignments for each domain:
  == domain 1  score: 409.8 bits;  conditional E-value: 4.8e-127
                             TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgld 77 
                                           ++g++++ + +++el +++ tP+Yvy+ + lr+ l++ ++  ++++ +v+YA+KAn+n  +l+ +++ G+g+d
  NCBI__GCF_002846395.1:WP_101445271.1   5 SKGTTTMLNLSVQEL-QQHATPFYVYNLNLLRQTLQRASQEAARYNFQVHYALKANTNSPILQEMRAVGFGAD 76 
                                           677778888888888.6799******************999999989************************** PP

                             TIGR01048  78 vvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnp 150
                                           +vsg E++ a + g++a+++vf+g+gks++e++ al+ +i ++n +s +el  l+e+a+  gk+ar++lR+np
  NCBI__GCF_002846395.1:WP_101445271.1  77 CVSGNEVKCAIENGFPAHHVVFAGVGKSDAEINYALDKDIFCFNCESSHELIVLNELAEAKGKTARIALRINP 149
                                           ************************************************************************* PP

                             TIGR01048 151 dvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelk 223
                                           +v+a+th+yi+TGl+e+KFGi+  e  ++  l ++l++l+l+G+h+HIGSqi+dl+ f++ + +v ++ + ++
  NCBI__GCF_002846395.1:WP_101445271.1 150 NVNANTHKYITTGLEENKFGINAWELPDVLALLKTLPNLSLIGLHFHIGSQITDLSAFKNLCTRVNEFQDWFE 222
                                           ************************************************************************* PP

                             TIGR01048 224 eegieleeldlGGGlgisyeeeeea..pdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVe 294
                                           +++++le++++GGGlg++y + +e+  pd e y + +++ l+       ++++ +E GR+lva++g+l+ rV 
  NCBI__GCF_002846395.1:WP_101445271.1 223 SQQVHLEHINVGGGLGVDYYNPDEQpiPDFEAYFSLFNQFLKV----RPNQQVHFELGRALVAQSGTLISRVL 291
                                           ******************9876643125667777776665555....5799********************** PP

                             TIGR01048 295 svKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdl 367
                                           ++K+  s++f++ Dagm++liRpalY++yh+i ++++  + ++e++dvvGp+CEs+D ++k + lpe+++Gdl
  NCBI__GCF_002846395.1:WP_101445271.1 292 YIKKGVSTNFAILDAGMTELIRPALYQSYHKIENISS--KGAEERYDVVGPICESSDCFGKAVVLPETNRGDL 362
                                           ***********************************66..6667****************************** PP

                             TIGR01048 368 lavasaGAYgasmssnYnsrprpaevl 394
                                           +a++ aGAYg  m+s Yn r ++a+v 
  NCBI__GCF_002846395.1:WP_101445271.1 363 IAIRTAGAYGEVMASAYNLRDKAAAVY 389
                                           ************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (391 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: 13.76
//
[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:

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