Alignments for a candidate for dapD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Herbaspirillum seropedicae SmR1

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate HSERO_RS10800 HSERO_RS10800 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__HerbieS:HSERO_RS10800
          Length = 277

 Score =  384 bits (986), Expect = e-111
 Identities = 195/273 (71%), Positives = 221/273 (80%), Gaps = 3/273 (1%)

Query: 2   QQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKID-GQWVTHQWLK 60
           Q +Q II+ A+E RA ++P +A    R AV +VIA L+ G LRVA +   GQW  +QW+K
Sbjct: 3   QSIQQIIDQAWEDRASLSPKSAPADIRNAVAEVIAGLNDGTLRVANRQGVGQWEVNQWVK 62

Query: 61  KAVLLSFRINDNQVIEGAES--RYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIA 118
           KA+LLSFR+ DN  +       +++DKVP KFA+Y    F K GFRVVPPA  R G+FI 
Sbjct: 63  KAILLSFRLEDNVPMSAGTGYPQFYDKVPTKFANYTAEDFAKGGFRVVPPAVARHGSFIG 122

Query: 119 RNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTII 178
           RN VLMPSYVNIGAYVDEGTMVDTWATVGS AQIGKNVHLSGGVGIGGVLEP+QA P II
Sbjct: 123 RNVVLMPSYVNIGAYVDEGTMVDTWATVGSAAQIGKNVHLSGGVGIGGVLEPVQAGPVII 182

Query: 179 EDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNL 238
           EDNCFIGARSEVVEGVI+EE SV+SMGVYIGQST+IYDRETGE+HYGRVPAGSVVV GNL
Sbjct: 183 EDNCFIGARSEVVEGVIIEENSVLSMGVYIGQSTKIYDRETGEVHYGRVPAGSVVVPGNL 242

Query: 239 PSKDGKYSLYCAVIVKKVDAKTRGKVGINELLR 271
           PSKDGKYSLY A+IVKKVDA+TR K  INELLR
Sbjct: 243 PSKDGKYSLYAAIIVKKVDAQTRSKTSINELLR 275


Lambda     K      H
   0.318    0.136    0.391 

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: 302
Number of extensions: 6
Number of successful extensions: 3
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: 274
Length of database: 277
Length adjustment: 25
Effective length of query: 249
Effective length of database: 252
Effective search space:    62748
Effective search space used:    62748
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: 47 (22.7 bits)

Align candidate HSERO_RS10800 HSERO_RS10800 (2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR00965.hmm
# target sequence database:        /tmp/gapView.23883.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00965  [M=271]
Accession:   TIGR00965
Description: dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.6e-143  463.0   0.9   1.8e-143  462.9   0.9    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS10800  HSERO_RS10800 2,3,4,5-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS10800  HSERO_RS10800 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransfe
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.9   0.9  1.8e-143  1.8e-143       2     270 ..       5     276 ..       4     277 .] 0.98

  Alignments for each domain:
  == domain 1  score: 462.9 bits;  conditional E-value: 1.8e-143
                                  TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfrit 68 
                                                +q+ii++a+e ra + p s+ +++++av e+ia l++g+lrva+++ +gqw vn+wvkka+llsfr++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10800   5 IQQIIDQAWEDRASLSPKSAPADIRNAVAEVIAGLNDGTLRVANRQgVGQWEVNQWVKKAILLSFRLE 72 
                                                89********************************************99******************** PP

                                  TIGR00965  69 dnqvln..davnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvde 134
                                                dn  +    ++ +++dkv+tkfa+y  + f + g+r+vp+av+r+g+fi +nvvlmpsyvnigayvde
  lcl|FitnessBrowser__HerbieS:HSERO_RS10800  73 DNVPMSagTGYPQFYDKVPTKFANYTAEDFAKGGFRVVPPAVARHGSFIGRNVVLMPSYVNIGAYVDE 140
                                                **8776125689******************************************************** PP

                                  TIGR00965 135 gtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvism 202
                                                gtmvdtwatvgs aqigknvhlsggvgiggvlep+qa pviiedncfigarse+vegvi+ee sv+sm
  lcl|FitnessBrowser__HerbieS:HSERO_RS10800 141 GTMVDTWATVGSAAQIGKNVHLSGGVGIGGVLEPVQAGPVIIEDNCFIGARSEVVEGVIIEENSVLSM 208
                                                ******************************************************************** PP

                                  TIGR00965 203 gvfigqstkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellrt 270
                                                gv+igqstki+dretge++ygrvpagsvvv+g+lpskdgk+sly a+ivkkvda+tr+k+sinellr+
  lcl|FitnessBrowser__HerbieS:HSERO_RS10800 209 GVYIGQSTKIYDRETGEVHYGRVPAGSVVVPGNLPSKDGKYSLYAAIIVKKVDAQTRSKTSINELLRG 276
                                                ******************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (277 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.87
//
[ok]

This GapMind analysis is from Apr 09 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