Alignments for a candidate for DAPtransferase in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for DAPtransferase in Crocosphaera subtropica ATCC 51142

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate WP_009544705.1 CCE_RS12335 LL-diaminopimelate aminotransferase

Query= BRENDA::Q3MAL4
         (411 letters)



>NCBI__GCF_000017845.1:WP_009544705.1
          Length = 411

 Score =  729 bits (1881), Expect = 0.0
 Identities = 350/411 (85%), Positives = 386/411 (93%)

Query: 1   MATINDNYLKLKAGYLFPEIARRVNAFAEANPDAKIIRLGIGDVTEPLPEACRTAMIQAV 60
           MATINDNYLKLKAGYLFPEIARRVN F EANP+AKII+LGIGDVTEPLPEACRTAMI+AV
Sbjct: 1   MATINDNYLKLKAGYLFPEIARRVNTFIEANPEAKIIKLGIGDVTEPLPEACRTAMIKAV 60

Query: 61  EEMGDRSSFKGYGPEQGYAWLREKIATQDFQARGADVDASEIFISDGSKCDTGNILDIFG 120
           E+MGDRSSFKGYGPEQGY WLREKIA QDFQARG D+DASEIF+SDG+KCDTGNILDIFG
Sbjct: 61  EDMGDRSSFKGYGPEQGYGWLREKIAAQDFQARGCDIDASEIFVSDGAKCDTGNILDIFG 120

Query: 121 DNNIIAVTDPVYPVYVDTNVMAGHTGVANDKGEFEGLVYLPVTAENNFTAEIPSQKVDLI 180
            NN IAVTDPVYPVYVDTNVMAGHTG  N+KGE+EGLVYLP++A+N+F A+IPS+KVDLI
Sbjct: 121 KNNKIAVTDPVYPVYVDTNVMAGHTGETNEKGEYEGLVYLPISADNHFVADIPSEKVDLI 180

Query: 181 YLCFPNNPTGATATKEHLQAWVDYAKAHNSIIFFDAAYESYITDPSLPHSIYEIEGAREV 240
           YLCFPNNPTGATATKE+L+AWVDYA A++SIIFFDAAYE++ITD SLPHSIYEIEGA++ 
Sbjct: 181 YLCFPNNPTGATATKEYLKAWVDYATANDSIIFFDAAYEAFITDESLPHSIYEIEGAKDC 240

Query: 241 AIEFRSFSKNAGFTGTRCALTVVPKTLKAKAADGSDVELWKLWNRRQSTKFNGVSYIVQR 300
           AIEFRSFSKNAGFTGTRCA TVVPK L AKA+DGS VELWKLWNRRQSTKFNGVSYIVQR
Sbjct: 241 AIEFRSFSKNAGFTGTRCAFTVVPKQLTAKASDGSQVELWKLWNRRQSTKFNGVSYIVQR 300

Query: 301 GAEAVYSEAGQAQVKALVSFYLDNAKIIREKLTAAGLSVYGGVNAPYVWVKTPNGLSSWD 360
           GAEAVYSEAG+AQ+K LVSFYL+NAKII E+L +AG  VYGGVNAPY+W+KTP+ LSSWD
Sbjct: 301 GAEAVYSEAGKAQIKGLVSFYLENAKIICEQLKSAGFEVYGGVNAPYIWLKTPHNLSSWD 360

Query: 361 FFDKLLQTVNVVGTPGSGFGAAGEGYFRISAFNSRENVEEAMQRITEKFKL 411
           FFDKLLQT +VVGTPGSGFGAAGEGYFRISAFNSRENVEEAM+RIT+ FK+
Sbjct: 361 FFDKLLQTTHVVGTPGSGFGAAGEGYFRISAFNSRENVEEAMKRITQAFKV 411


Lambda     K      H
   0.317    0.134    0.397 

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: 25
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: 411
Length of database: 411
Length adjustment: 31
Effective length of query: 380
Effective length of database: 380
Effective search space:   144400
Effective search space used:   144400
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: 50 (23.9 bits)

Align candidate WP_009544705.1 CCE_RS12335 (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.6989.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-188  611.5   0.3   3.9e-188  611.3   0.3    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009544705.1  CCE_RS12335 LL-diaminopimelate a


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009544705.1  CCE_RS12335 LL-diaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.3   0.3  3.9e-188  3.9e-188       2     401 ..       3     408 ..       2     409 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.3 bits;  conditional E-value: 3.9e-188
                                 TIGR03542   2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 
                                               ++n+++lklk++ylf+eia++v++f ++npea+ii+lgiGdvt+Pl++a+  a+ +ave++ ++ +f+G
  lcl|NCBI__GCF_000017845.1:WP_009544705.1   3 TINDNYLKLKAGYLFPEIARRVNTFIEANPEAKIIKLGIGDVTEPLPEACRTAMIKAVEDMGDRSSFKG 71 
                                               68******************************************************************* PP

                                 TIGR03542  71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136
                                               yGpeqG+ +lre+ia +++++r   id++eif+sdGakcd++++l++fg+++++av+dPvyPvyvd++v
  lcl|NCBI__GCF_000017845.1:WP_009544705.1  72 YGPEQGYGWLREKIAAQDFQARgcdIDASEIFVSDGAKCDTGNILDIFGKNNKIAVTDPVYPVYVDTNV 140
                                               ********************************************************************* PP

                                 TIGR03542 137 laGragvldddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyaken 205
                                               +aG++g+ +++g+y+ +vylp  ++n+f+ ++p+ek vd+iylC+PnnPtG+++tke lk++vdya++n
  lcl|NCBI__GCF_000017845.1:WP_009544705.1 141 MAGHTGETNEKGEYEGLVYLPISADNHFVADIPSEK-VDLIYLCFPNNPTGATATKEYLKAWVDYATAN 208
                                               ***********************************9.******************************** PP

                                 TIGR03542 206 dslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....e 270
                                               ds+i+fdaayeafi+d+slP+siyeiegak caie+rsfsk++GftG+r+++tvvPk+l+++ +     
  lcl|NCBI__GCF_000017845.1:WP_009544705.1 209 DSIIFFDAAYEAFITDESLPHSIYEIEGAKDCAIEFRSFSKNAGFTGTRCAFTVVPKQLTAKASdgsqV 277
                                               ***********************************************************9887666767 PP

                                 TIGR03542 271 slkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaP 339
                                               +l klW+r+++tkfnG+s+ivqr+aeav++++g+ qik ++s y+ena+i+ ++l++ag++vyGG+naP
  lcl|NCBI__GCF_000017845.1:WP_009544705.1 278 ELWKLWNRRQSTKFNGVSYIVQRGAEAVYSEAGKAQIKGLVSFYLENAKIICEQLKSAGFEVYGGVNAP 346
                                               889****************************************************************** PP

                                 TIGR03542 340 ylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerikea 401
                                               y+W+k+p+++ss+dffdkll++++vvgtPGsGfG++GeG++r+sa+++re++ ea++ri++a
  lcl|NCBI__GCF_000017845.1:WP_009544705.1 347 YIWLKTPHNLSSWDFFDKLLQTTHVVGTPGSGFGAAGEGYFRISAFNSRENVEEAMKRITQA 408
                                               ***********************************************************975 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.81
//
[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