Alignments for a candidate for dapC in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Amycolatopsis halophila YIM 93223

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate WP_034275069.1 AMYHA_RS24965 succinyldiaminopimelate transaminase

Query= BRENDA::Q8NRE6
         (367 letters)



>NCBI__GCF_000504245.1:WP_034275069.1
          Length = 365

 Score =  425 bits (1092), Expect = e-123
 Identities = 215/360 (59%), Positives = 264/360 (73%), Gaps = 4/360 (1%)

Query: 9   SVLPDFPWDSLASAKAKAASHPDGIVNLSVGTPVDPVAPSIQIALAEAAGFSGYPQTIGT 68
           S LPDFPWDSL     KA SHP GIV+LSVGTPVDPVAP IQ ALA  A   GYP T GT
Sbjct: 6   SALPDFPWDSLTPYGDKARSHPGGIVDLSVGTPVDPVAPEIQQALASVAEVPGYPATHGT 65

Query: 69  PELRAAIRGALERRYNMTKLVDASLLPVVGTKEAIALLPFALGISG--TVVIPEIAYPTY 126
           PELRAAIR AL RR+   ++   ++LP VG+KE +ALLP  LG+     VVIPE+AYPTY
Sbjct: 66  PELRAAIRDALVRRHGAAEIEPDAVLPTVGSKELVALLPRLLGLGDGDVVVIPELAYPTY 125

Query: 127 EVAVVAAGCTVLRSDSLFKLGPQIPSMMFINSPSNPTGKVLGIPHLRKVVKWAQENNVIL 186
           EV  + AG  V R+DSL +LGP+ P+++++NSPSNPTG+VLG+ HLRKVV+WA+E   ++
Sbjct: 126 EVGALLAGGEVRRADSLTQLGPERPALLWLNSPSNPTGRVLGVEHLRKVVEWARERGTVV 185

Query: 187 AADECYLGLGWDDENPPISILDPRVCDGDHTNLIAIHSLSKTSNLASYRAGYLVGDPALI 246
           A+DECYL LGWD E  P+S+L P V  G    L+A+HSLSK++NLA YRAG++ GDP L+
Sbjct: 186 ASDECYLALGWDSE--PVSVLHPDVNGGSLDGLLAVHSLSKSANLAGYRAGFVTGDPRLV 243

Query: 247 GELTEVRKNLGLMVPFPIQQAMIAALNDDDQEAGQKLTYAIRRAKLMRALLESGFQVDNS 306
            +L  VRK+ GL+VP P+Q AM AAL  DD  A Q+  YA RR  L + L  +GF++D+S
Sbjct: 244 ADLLAVRKHAGLIVPRPVQAAMTAALGADDALAAQQGKYAARRDTLRKVLQSAGFRIDHS 303

Query: 307 EAGLYLWATREEPCRDTVDWFAERGILVAPGDFYGPRGAQHVRVAMTETDERVDAFVSRL 366
           EAGLYLW TR+E    TVDWFAERGILVAPG FYGP G +HVRV +T TDERV    +RL
Sbjct: 304 EAGLYLWVTRDEDAWQTVDWFAERGILVAPGTFYGPAGGKHVRVGLTATDERVREAATRL 363


Lambda     K      H
   0.319    0.135    0.403 

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: 444
Number of extensions: 19
Number of successful extensions: 4
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: 367
Length of database: 365
Length adjustment: 30
Effective length of query: 337
Effective length of database: 335
Effective search space:   112895
Effective search space used:   112895
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: 49 (23.5 bits)

Align candidate WP_034275069.1 AMYHA_RS24965 (succinyldiaminopimelate transaminase)
to HMM TIGR03539 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03539.hmm
# target sequence database:        /tmp/gapView.864986.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03539  [M=357]
Accession:   TIGR03539
Description: DapC_actino: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-180  585.3   0.6   2.5e-180  585.1   0.6    1.0  1  NCBI__GCF_000504245.1:WP_034275069.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034275069.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  585.1   0.6  2.5e-180  2.5e-180       1     356 [.       8     363 ..       8     364 .. 1.00

  Alignments for each domain:
  == domain 1  score: 585.1 bits;  conditional E-value: 2.5e-180
                             TIGR03539   1 lPdfPWdklaeakakaashpdGivdlsvGtPvdpvpalirealaeaadapgyPqtaGteelreaivdalerrl 73 
                                           lPdfPWd+l+++ +ka+shp+GivdlsvGtPvdpv++ i++ala++a++pgyP t+Gt+elr+ai dal rr+
  NCBI__GCF_000504245.1:WP_034275069.1   8 LPDFPWDSLTPYGDKARSHPGGIVDLSVGTPVDPVAPEIQQALASVAEVPGYPATHGTPELRAAIRDALVRRH 80 
                                           8************************************************************************ PP

                             TIGR03539  74 gvkgldeeavlPviGtkelvallPtllGlgagdtvviPevayPtyevgarlagaeavaaddlteldpekvkli 146
                                           g+  ++++avlP++G+kelvallP+llGlg gd+vviPe+ayPtyevga lag e+ +ad+lt+l+pe+++l+
  NCBI__GCF_000504245.1:WP_034275069.1  81 GAAEIEPDAVLPTVGSKELVALLPRLLGLGDGDVVVIPELAYPTYEVGALLAGGEVRRADSLTQLGPERPALL 153
                                           ************************************************************************* PP

                             TIGR03539 147 wlnsPanPtGrvlsveelrkvvalarergvvvasdecylelgWegeavsvldpevcggdlegllavhslskrs 219
                                           wlnsP+nPtGrvl+ve+lrkvv++arerg+vvasdecyl lgW++e+vsvl+p+v+gg+l+gllavhslsk++
  NCBI__GCF_000504245.1:WP_034275069.1 154 WLNSPSNPTGRVLGVEHLRKVVEWARERGTVVASDECYLALGWDSEPVSVLHPDVNGGSLDGLLAVHSLSKSA 226
                                           ************************************************************************* PP

                             TIGR03539 220 nlagyragfvaGdealvaellevrkhaGlmvpaPvqaamvaaladdehvaeqkeryaarrellkaalekaGfr 292
                                           nlagyragfv+Gd+ lva+ll+vrkhaGl+vp Pvqaam+aal+ d+  a+q+ +yaarr++l++ l++aGfr
  NCBI__GCF_000504245.1:WP_034275069.1 227 NLAGYRAGFVTGDPRLVADLLAVRKHAGLIVPRPVQAAMTAALGADDALAAQQGKYAARRDTLRKVLQSAGFR 299
                                           ************************************************************************* PP

                             TIGR03539 293 iehseaglylWatrgedaretvdrlaelGilvaPGdfygeagkefvrvaltatderiaaaverl 356
                                           i+hseaglylW tr+eda++tvd++ae+GilvaPG+fyg+ag ++vrv+ltatder+ +a++rl
  NCBI__GCF_000504245.1:WP_034275069.1 300 IDHSEAGLYLWVTRDEDAWQTVDWFAERGILVAPGTFYGPAGGKHVRVGLTATDERVREAATRL 363
                                           ***************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (365 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: 00:00:00.00
# Mc/sec: 20.61
//
[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:

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 2024 update 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 original 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