Alignments for a candidate for DAPtransferase in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Malonomonas rubra DSM 5091

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_072909617.1 BUB13_RS15180 LL-diaminopimelate aminotransferase

Query= BRENDA::Q74GT3
         (410 letters)



>NCBI__GCF_900142125.1:WP_072909617.1
          Length = 411

 Score =  690 bits (1781), Expect = 0.0
 Identities = 331/407 (81%), Positives = 359/407 (88%)

Query: 1   MAKINDHYLKLKAGYLFPEIGRRVREFAAANPSAKVIRLGIGDVTRPLAPAVIKAFHEAV 60
           MA+IND+YLKL+AGYLFPEI RRV+ F  ANP AKVIRLGIGDVTRPL PAV+KAFHE V
Sbjct: 1   MARINDNYLKLQAGYLFPEISRRVKAFTDANPDAKVIRLGIGDVTRPLVPAVLKAFHEGV 60

Query: 61  DDLATTENFAGYGPEQGYDWLINAIIEKSYKPLGVDLKTEEMFISDGSKCDCANILDIFA 120
           DDLA  E F GYGPEQGY WL   + EK+YKPLGV+LKT E+FISDGSKCD AN+LDIF 
Sbjct: 61  DDLAKGETFHGYGPEQGYSWLAEVVAEKAYKPLGVELKTSEIFISDGSKCDSANLLDIFD 120

Query: 121 LDNVVAIGDPVYPVYNDTNVMIGRTGEADDKGYYKGIVYMPCTEENGFIPSLPTEKVDII 180
           L N VAIGDPVYPVYNDTNVMIGRTG+A++KGYY+GIVYMPCTEEN F P LP EKVDII
Sbjct: 121 LGNKVAIGDPVYPVYNDTNVMIGRTGKANEKGYYEGIVYMPCTEENNFTPELPKEKVDII 180

Query: 181 YLCFPNNPTGTVATKAELKKWVDYAIANDAVIFFDAAYEAFITDPAIPHSIYEIEGAKKC 240
           YLC PNNPTGT A+K ELK+WVDYA ANDA+IFFDAAYEAFIT   IPHSIYEIEGAK+C
Sbjct: 181 YLCSPNNPTGTAASKEELKQWVDYARANDAIIFFDAAYEAFITQADIPHSIYEIEGAKEC 240

Query: 241 AIEFRSFSKTAGFTGVRCGLVVVPEEVMGTTPTGEKYSFNKLWLRRTTTKFNGASYPVQK 300
           AIE RSFSKTAGFTGVRCG +VVPE +MGTT TGE+YSFNKLW RRT+TKFNGASYPVQK
Sbjct: 241 AIEIRSFSKTAGFTGVRCGFIVVPEALMGTTETGERYSFNKLWSRRTSTKFNGASYPVQK 300

Query: 301 AAAAVYSDEGWQQNKEIIDYYMENARIIREGLAAAGLTVYGGVNAPYIWLKTPGGMSSWD 360
           AAAAVYSDEGW Q +E+IDYYMENARIIREGL  AG+T YGGVNAPYIWLKTP GMSSWD
Sbjct: 301 AAAAVYSDEGWAQVQEVIDYYMENARIIREGLTEAGITCYGGVNAPYIWLKTPEGMSSWD 360

Query: 361 FFDKLLNECNVVGTPGSGFGPSGEGFFRLSAFGHRENVIEAVERIKK 407
           FFDKLLNEC VVGTPGSGFGPSGEG+FRLSAFG RENV  AV RI++
Sbjct: 361 FFDKLLNECFVVGTPGSGFGPSGEGYFRLSAFGDRENVETAVSRIRE 407


Lambda     K      H
   0.319    0.138    0.422 

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: 680
Number of extensions: 19
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: 410
Length of database: 411
Length adjustment: 31
Effective length of query: 379
Effective length of database: 380
Effective search space:   144020
Effective search space used:   144020
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_072909617.1 BUB13_RS15180 (LL-diaminopimelate aminotransferase)
to HMM TIGR03542 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))

# 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/TIGR03542.hmm
# target sequence database:        /tmp/gapView.13026.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03542  [M=402]
Accession:   TIGR03542
Description: DAPAT_plant: LL-diaminopimelate aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-196  637.6   0.0   4.4e-196  637.4   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072909617.1  BUB13_RS15180 LL-diaminopimelate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072909617.1  BUB13_RS15180 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  637.4   0.0  4.4e-196  4.4e-196       2     401 ..       3     408 ..       2     409 .. 0.99

  Alignments for each domain:
  == domain 1  score: 637.4 bits;  conditional E-value: 4.4e-196
                                 TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 
                                               ++n+++lkl+++ylf+ei+++vk f  +np+a++irlgiGdvt+Pl +av +a++e v++la+ etf G
  lcl|NCBI__GCF_900142125.1:WP_072909617.1   3 RINDNYLKLQAGYLFPEISRRVKAFTDANPDAKVIRLGIGDVTRPLVPAVLKAFHEGVDDLAKGETFHG 71 
                                               79******************************************************************* PP

                                 TIGR03542  71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136
                                               yGpeqG+++l e +ae+ yk+    ++++eifisdG+kcd a+ll++f   ++va+ dPvyPvy+d++v
  lcl|NCBI__GCF_900142125.1:WP_072909617.1  72 YGPEQGYSWLAEVVAEKAYKPLgveLKTSEIFISDGSKCDSANLLDIFDLGNKVAIGDPVYPVYNDTNV 140
                                               *********************9999******************************************** PP

                                 TIGR03542 137 laGragvldddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyaken 205
                                               ++Gr+g+++++g+y+ ivy+pct+en+f Pelp+ek vdiiylCsPnnPtGt+++ke+lk++vdya++n
  lcl|NCBI__GCF_900142125.1:WP_072909617.1 141 MIGRTGKANEKGYYEGIVYMPCTEENNFTPELPKEK-VDIIYLCSPNNPTGTAASKEELKQWVDYARAN 208
                                               ***********************************9.******************************** PP

                                 TIGR03542 206 dslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....e 270
                                               d++i+fdaayeafi++ ++P+siyeiegakecaieirsfskt+GftGvr+g+ vvP+ l+ +++    +
  lcl|NCBI__GCF_900142125.1:WP_072909617.1 209 DAIIFFDAAYEAFITQADIPHSIYEIEGAKECAIEIRSFSKTAGFTGVRCGFIVVPEALMGTTEtgerY 277
                                               ***********************************************************9888778889 PP

                                 TIGR03542 271 slkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaP 339
                                               s++klW r+++tkfnGas++vq+aa+av+++eg+ q +e+i+yymenari+r++l++ag++ yGG+naP
  lcl|NCBI__GCF_900142125.1:WP_072909617.1 278 SFNKLWSRRTSTKFNGASYPVQKAAAAVYSDEGWAQVQEVIDYYMENARIIREGLTEAGITCYGGVNAP 346
                                               ********************************************************************* PP

                                 TIGR03542 340 ylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerikea 401
                                               y+W+k+peg+ss+dffdkll+e+ vvgtPGsGfG+sGeG++rlsa+g+re++ +a++ri+e+
  lcl|NCBI__GCF_900142125.1:WP_072909617.1 347 YIWLKTPEGMSSWDFFDKLLNECFVVGTPGSGFGPSGEGYFRLSAFGDRENVETAVSRIREK 408
                                               ***********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (402 nodes)
Target sequences:                          1  (411 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.60
//
[ok]

This GapMind analysis is from Apr 10 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