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.14910.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.68
//
[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:

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:

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:

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:

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