Alignments for a candidate for lysA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Dinoroseobacter shibae DFL-12

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 3609676 Dshi_3059 diaminopimelate decarboxylase (RefSeq)

Query= reanno::Korea:Ga0059261_2051
         (419 letters)



>FitnessBrowser__Dino:3609676
          Length = 431

 Score =  412 bits (1058), Expect = e-119
 Identities = 217/422 (51%), Positives = 280/422 (66%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           MDHF    G LHAE+V + AIA  VGTP YVYSTATL RH      AL+  P + + FA+
Sbjct: 1   MDHFTYIKGQLHAEDVPVSAIADAVGTPFYVYSTATLTRHFKLFDEALSWGPHL-VCFAM 59

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           K+N N A+L +LA  G G DVVSGGE  RA AAG+P + +VFSGVGKT  E+++ L  GI
Sbjct: 60  KSNSNQAILKLLADLGAGMDVVSGGEYARARAAGVPGDRIVFSGVGKTADEMRMALTGGI 119

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
            QFN+E E E + L+ +A   G  AP  +RVNPDVDA TH KI+TGK+ENKFG+ I RA 
Sbjct: 120 RQFNVESEPEMQRLSAVAQGLGMQAPITIRVNPDVDAKTHEKIATGKSENKFGIPISRAR 179

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
           E++ + A+ PG+ + G+ +HIGSQLTEL P E AY +V EL   LRA GH IT +DLGGG
Sbjct: 180 EVYAQAARLPGIKVIGIDVHIGSQLTELEPFELAYAKVAELTRHLRADGHEITRLDLGGG 239

Query: 241 LGVPY-HAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299
           LG+PY    +      ++GA++ R        +  EPGR I GNAG+LV+EVI+VK    
Sbjct: 240 LGIPYARTNEAPPLPTDYGALIQRTVGDLGCEIEIEPGRLISGNAGLLVSEVIYVKQGED 299

Query: 300 NPYVIVDAAMNDLARPALYDAYHEFEAVE---PTGEKFVANIAGPVCETGDTFAMGREID 356
             ++I+DAAMNDL RP++Y AYH+   V    P       +I GPVCE+GDTFA  RE+ 
Sbjct: 300 RQFLILDAAMNDLIRPSMYGAYHDIVPVREAAPGTPTTPYDIVGPVCESGDTFAKSREMV 359

Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416
            +  GDL  FR+AGAYGA MAS YN+R L+PEVLV GD+FAV+  R   + I+  + +P 
Sbjct: 360 PLTEGDLVAFRSAGAYGAVMASEYNTRPLIPEVLVHGDQFAVIRQRPSFDEIINRDTIPA 419

Query: 417 WV 418
           W+
Sbjct: 420 WL 421


Lambda     K      H
   0.318    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: 542
Number of extensions: 20
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: 419
Length of database: 431
Length adjustment: 32
Effective length of query: 387
Effective length of database: 399
Effective search space:   154413
Effective search space used:   154413
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: 51 (24.3 bits)

Align candidate 3609676 Dshi_3059 (diaminopimelate decarboxylase (RefSeq))
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.16898.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-147  477.7   0.0   1.4e-147  477.4   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609676  Dshi_3059 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609676  Dshi_3059 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.4   0.0  1.4e-147  1.4e-147       6     416 ..       8     415 ..       4     416 .. 0.96

  Alignments for each domain:
  == domain 1  score: 477.4 bits;  conditional E-value: 1.4e-147
                         TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                       +g+l +e+v++ ++a+  gtP+Yvy+++tl+++++ ++ea +   +lv++A+K+nsn a+l+lla++G+g+dvvsgG
  lcl|FitnessBrowser__Dino:3609676   8 KGQLHAEDVPVSAIADAVGTPFYVYSTATLTRHFKLFDEALSWGPHLVCFAMKSNSNQAILKLLADLGAGMDVVSGG 84 
                                       799***************************************999******************************** PP

                         TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthey 159
                                       E +ra aAgv+ ++ivfsg+gk+ +e+++al+ +i+ +nv+s+ e+++l+++a++lg++a++++Rvnpdvdakthe+
  lcl|FitnessBrowser__Dino:3609676  85 EYARARAAGVPGDRIVFSGVGKTADEMRMALTGGIRQFNVESEPEMQRLSAVAQGLGMQAPITIRVNPDVDAKTHEK 161
                                       ***************************************************************************** PP

                         TIGR01048 160 isTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGG 236
                                       i+TG+ e+KFGi +++a+e+y +a++l+ ++++Gi+vHIGSq+++lepf+ a +kv++l+++l+++g e++ ldlGG
  lcl|FitnessBrowser__Dino:3609676 162 IATGKSENKFGIPISRAREVYAQAARLPGIKVIGIDVHIGSQLTELEPFELAYAKVAELTRHLRADGHEITRLDLGG 238
                                       ***************************************************************************** PP

                         TIGR01048 237 Glgisyeeeeea.pdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmn 312
                                       Glgi+y + +ea p +++y + + +++ +     l  ++ +EpGR + +nag l+ +V +vK+ e r+f + Da+mn
  lcl|FitnessBrowser__Dino:3609676 239 GLGIPYARTNEApPLPTDYGALIQRTVGD-----LGCEIEIEPGRLISGNAGLLVSEVIYVKQGEDRQFLILDAAMN 310
                                       ******98766505578888888877777.....799**************************************** PP

                         TIGR01048 313 dliRpalYeayheiaalkr.leeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrp 388
                                       dliRp++Y+ayh+i+++++    ++t+ +d+vGp+CEsgD++ak re+    eGdl+a +saGAYga m+s+Yn+rp
  lcl|FitnessBrowser__Dino:3609676 311 DLIRPSMYGAYHDIVPVREaAPGTPTTPYDIVGPVCESGDTFAKSREMVPLTEGDLVAFRSAGAYGAVMASEYNTRP 387
                                       *****************8835578999************************************************** PP

                         TIGR01048 389 rpaevlveegkarlirrretledllale 416
                                        + evlv++++  +ir+r +++++++ +
  lcl|FitnessBrowser__Dino:3609676 388 LIPEVLVHGDQFAVIRQRPSFDEIINRD 415
                                       ************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (431 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.43
//
[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