Alignments for a candidate for lysA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Magnetospirillum magneticum AMB-1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_011386835.1 AMB_RS22725 diaminopimelate decarboxylase

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



>NCBI__GCF_000009985.1:WP_011386835.1
          Length = 424

 Score =  406 bits (1044), Expect = e-118
 Identities = 221/423 (52%), Positives = 285/423 (67%), Gaps = 7/423 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNAL--AGLPSVHLAF 58
           M+HF+ +NG L AE+V+I  IA EVGTP Y YSTATL+RH +    AL  AGL +  + F
Sbjct: 1   MNHFHYQNGELFAEDVAIARIAREVGTPFYCYSTATLQRHYTVFAEALKAAGLDAT-ICF 59

Query: 59  AIKANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDE 118
           A KANPN+AV+   A+ G GADVVS GEL++ALAAG+PA  +VFSGVGKTR EL+  + +
Sbjct: 60  AAKANPNMAVIRTFAQLGAGADVVSEGELRQALAAGVPAARIVFSGVGKTRHELEFAVAK 119

Query: 119 GIGQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDR 178
           GI Q N+E E E E+L+++A A+G+  P  +RVNPDVDAGTHAKI+TGK ENKFG+   R
Sbjct: 120 GIFQINVESEPELEMLSEIAAARGQVMPIAIRVNPDVDAGTHAKITTGKKENKFGIEWTR 179

Query: 179 ALEIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLG 238
           A E++ R    PG+    +A HIGSQLTEL P   A+ RV +LVA LRA G  I  +DLG
Sbjct: 180 AREVYARAKALPGVEPVAIACHIGSQLTELTPFREAFLRVRDLVAMLRADGIDIRRLDLG 239

Query: 239 GGLGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAA 298
           GGLGVPY   +T      +  ++           +FEPGR + GNAG+LV+ +I VK  +
Sbjct: 240 GGLGVPYD-DETPPEPAAYAEVIKATLGDLGCRFVFEPGRLLVGNAGILVSRIIRVKEGS 298

Query: 299 GNPYVIVDAAMNDLARPALYDAYHE-FEAVEPTGEKFVA--NIAGPVCETGDTFAMGREI 355
              ++IVDAAMNDLARP+LYDAYH  F   EP     +A  ++ GPVCETGDTFA  R +
Sbjct: 299 TRTFLIVDAAMNDLARPSLYDAYHSIFPVAEPKAGAALAEVDVVGPVCETGDTFAKQRRL 358

Query: 356 DVVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVP 415
             +++ DL  F TAGAYGA M+STYN+R L+PEVLV G  +AV+  R   E +   E +P
Sbjct: 359 PPMRTDDLLAFGTAGAYGAAMSSTYNTRPLIPEVLVKGGDYAVIRVRPSYEDMRSLESLP 418

Query: 416 EWV 418
            W+
Sbjct: 419 GWL 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: 530
Number of extensions: 23
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: 424
Length adjustment: 32
Effective length of query: 387
Effective length of database: 392
Effective search space:   151704
Effective search space used:   151704
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: 50 (23.9 bits)

Align candidate WP_011386835.1 AMB_RS22725 (diaminopimelate decarboxylase)
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.23773.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-145  470.6   0.0   2.1e-145  470.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386835.1  AMB_RS22725 diaminopimelate deca


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386835.1  AMB_RS22725 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.3   0.0  2.1e-145  2.1e-145       4     416 ..       6     415 ..       4     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 470.3 bits;  conditional E-value: 2.1e-145
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrlla 70 
                                                ++gel++e+v+++++a+e gtP+Y y+++tl+++++ ++ea ka   ++++++A+KAn n+av+r++a
  lcl|NCBI__GCF_000009985.1:WP_011386835.1   6 YQNGELFAEDVAIARIAREVGTPFYCYSTATLQRHYTVFAEALKAagLDATICFAAKANPNMAVIRTFA 74 
                                               589****************************************9965556******************* PP

                                 TIGR01048  71 eeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelg 139
                                               ++G+g+dvvs+GEl +alaAgv+a +ivfsg+gk+++ele a++ +i  inv+s+ ele+l+eia+  g
  lcl|NCBI__GCF_000009985.1:WP_011386835.1  75 QLGAGADVVSEGELRQALAAGVPAARIVFSGVGKTRHELEFAVAKGIFQINVESEPELEMLSEIAAARG 143
                                               ********************************************************************* PP

                                 TIGR01048 140 kkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepf 208
                                               + +++++Rvnpdvda th +i+TG+ke+KFGie ++a+e+y +a++l+ +e+v i +HIGSq+++l pf
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 144 QVMPIAIRVNPDVDAGTHAKITTGKKENKFGIEWTRAREVYARAKALPGVEPVAIACHIGSQLTELTPF 212
                                               ********************************************************************* PP

                                 TIGR01048 209 veaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilE 277
                                               +ea+ +v +l++ l+++gi+++ ldlGGGlg++y++e+ +p+++ yae+++++l +     l  + ++E
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 213 REAFLRVRDLVAMLRADGIDIRRLDLGGGLGVPYDDET-PPEPAAYAEVIKATLGD-----LGCRFVFE 275
                                               ************************************99.************99999.....7999**** PP

                                 TIGR01048 278 pGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrlee.eetetvdvvGp 345
                                               pGR lv+nag+l+ r+  vKe ++r+f +vDa+mndl Rp+lY+ayh+i+++++ ++ ++ ++vdvvGp
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 276 PGRLLVGNAGILVSRIIRVKEGSTRTFLIVDAAMNDLARPSLYDAYHSIFPVAEPKAgAALAEVDVVGP 344
                                               ****************************************************99776155689****** PP

                                 TIGR01048 346 lCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414
                                               +CE+gD++ak+r+lp ++++dlla   aGAYga+mss+Yn+rp + evlv++g++ +ir r ++ed+ +
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 345 VCETGDTFAKQRRLPPMRTDDLLAFGTAGAYGAAMSSTYNTRPLIPEVLVKGGDYAVIRVRPSYEDMRS 413
                                               ******************************************************************977 PP

                                 TIGR01048 415 le 416
                                               le
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 414 LE 415
                                               65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (424 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: 8.24
//
[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