Alignments for a candidate for dapB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Pedobacter sp. GW460-11-11-14-LB5

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate CA265_RS15670 CA265_RS15670 4-hydroxy-tetrahydrodipicolinate reductase

Query= reanno::Pedo557:CA265_RS15670
         (244 letters)



>FitnessBrowser__Pedo557:CA265_RS15670
          Length = 244

 Score =  489 bits (1260), Expect = e-143
 Identities = 244/244 (100%), Positives = 244/244 (100%)

Query: 1   MKLALLGYGKMGQIIEKFAVERGHEIVLKITIDNQEDLTRQNLKSADVAIDFSTPDSVLK 60
           MKLALLGYGKMGQIIEKFAVERGHEIVLKITIDNQEDLTRQNLKSADVAIDFSTPDSVLK
Sbjct: 1   MKLALLGYGKMGQIIEKFAVERGHEIVLKITIDNQEDLTRQNLKSADVAIDFSTPDSVLK 60

Query: 61  NIDACFDANVPIVVGTTGWYGKLQEVKDDCNNSNNTLLYGSNFSIGVNLFFKLNQTLAKL 120
           NIDACFDANVPIVVGTTGWYGKLQEVKDDCNNSNNTLLYGSNFSIGVNLFFKLNQTLAKL
Sbjct: 61  NIDACFDANVPIVVGTTGWYGKLQEVKDDCNNSNNTLLYGSNFSIGVNLFFKLNQTLAKL 120

Query: 121 MNNYPAYEVQVEEIHHTQKLDAPSGTAITLAEGIVDNLDRKQEWLNEVVGTDVELFPKAE 180
           MNNYPAYEVQVEEIHHTQKLDAPSGTAITLAEGIVDNLDRKQEWLNEVVGTDVELFPKAE
Sbjct: 121 MNNYPAYEVQVEEIHHTQKLDAPSGTAITLAEGIVDNLDRKQEWLNEVVGTDVELFPKAE 180

Query: 181 QLLIESHRIENIPGTHTVIYSSEVDEIEIKHTAHNRAGFALGAVVAAEWLKDKKGFFSIT 240
           QLLIESHRIENIPGTHTVIYSSEVDEIEIKHTAHNRAGFALGAVVAAEWLKDKKGFFSIT
Sbjct: 181 QLLIESHRIENIPGTHTVIYSSEVDEIEIKHTAHNRAGFALGAVVAAEWLKDKKGFFSIT 240

Query: 241 DIFE 244
           DIFE
Sbjct: 241 DIFE 244


Lambda     K      H
   0.317    0.135    0.389 

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: 352
Number of extensions: 5
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: 244
Length of database: 244
Length adjustment: 24
Effective length of query: 220
Effective length of database: 220
Effective search space:    48400
Effective search space used:    48400
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate CA265_RS15670 CA265_RS15670 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

# 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/TIGR00036.hmm
# target sequence database:        /tmp/gapView.18589.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00036  [M=270]
Accession:   TIGR00036
Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    7.5e-50  155.9   0.1      1e-49  155.5   0.1    1.2  1  lcl|FitnessBrowser__Pedo557:CA265_RS15670  CA265_RS15670 4-hydroxy-tetrahyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15670  CA265_RS15670 4-hydroxy-tetrahydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.1     1e-49     1e-49      58     269 ..      30     243 ..       3     244 .] 0.84

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 1e-49
                                  TIGR00036  58 veddleavkvla.ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgva 124
                                                ++ d + + + +  k+adv iDf+tp++vl+n+ ++ +++v +VvGTTG    +l+e+kd  ++++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS15670  30 ITIDNQEDLTRQnLKSADVAIDFSTPDSVLKNIDACFDANVPIVVGTTGWYG-KLQEVKDDCNNSNNT 96 
                                                33333333333337899********************************986.689999999999*** PP

                                  TIGR00036 125 lviapNfaiGvnlllkllekaakvledv...DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlk. 188
                                                l++ +Nf+iGvnl++kl +++ak ++++   ++ + E+HH +K DaPSGTA+ lae i ++ +++++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS15670  97 LLYGSNFSIGVNLFFKLNQTLAKLMNNYpayEVQVEEIHHTQKLDAPSGTAITLAEGIVDNLDRKQEw 164
                                                **************************9876689999***********************999953331 PP

                                  TIGR00036 189 ..eaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairw 254
                                                  e++ +  e +    k+e+  i + R  ++ g htv++ s+ + +ei+H+a++Ra fa G+v a++w
  lcl|FitnessBrowser__Pedo557:CA265_RS15670 165 lnEVVGTDVELF--P-KAEQLLIESHRIENIPGTHTVIYSSEVDEIEIKHTAHNRAGFALGAVVAAEW 229
                                                102222333333..3.589999********************************************** PP

                                  TIGR00036 255 ledkeekvydledvl 269
                                                l+dk+ +++ ++d++
  lcl|FitnessBrowser__Pedo557:CA265_RS15670 230 LKDKK-GFFSITDIF 243
                                                *9975.789999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (244 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: 2.85
//
[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