Alignments for a candidate for lysA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Herbaspirillum seropedicae SmR1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate HSERO_RS00950 HSERO_RS00950 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__HerbieS:HSERO_RS00950
          Length = 430

 Score =  467 bits (1201), Expect = e-136
 Identities = 233/430 (54%), Positives = 319/430 (74%), Gaps = 16/430 (3%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSV--------GDY 52
           M +F+Y+ +G L AEQV LA LA Q+GTPLYVYS+A L  ++ A+  +         G  
Sbjct: 1   MSHFSYR-NGVLHAEQVSLATLAEQFGTPLYVYSKAALVENFSAYANACQQAGRADGGKG 59

Query: 53  PHLICYAVKANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEM 112
             L+CY+VK+NSNL VLN L RLGSGFDIVS GEL RV+AAGGD  KV+FSGVGK   EM
Sbjct: 60  GALVCYSVKSNSNLAVLNLLGRLGSGFDIVSGGELLRVVAAGGDARKVIFSGVGKGRDEM 119

Query: 113 KRALQLKIKCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKF 172
           K AL+  I CFNVES PE+ RLN+VAG LG +A ISLR+NP+VDAKTHPYISTGL++NKF
Sbjct: 120 KLALEHDILCFNVESIPEVARLNEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKF 179

Query: 173 GITFDRAAQVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHI 232
           G+ ++ A   YR A +LP+++V GIDCHIGSQL   +P ++A D+++ ++D+L+AEGI I
Sbjct: 180 GVAYEDALNCYRAAAALPHIEVVGIDCHIGSQLLDDSPLLEALDKIIDMVDALEAEGIPI 239

Query: 233 RHLDVGGGLGVVYRDELPPQPSEYAKALLDRLE-------RHRDLELIFEPGRAIAANAG 285
            HLD+GGG+G+ Y DE P    +Y   +  R++       + R ++++FEPGR++  NAG
Sbjct: 240 HHLDIGGGIGIRYDDEQPVAIGDYLARVFARVDAWRASKYQGRPIQVMFEPGRSVVGNAG 299

Query: 286 VLVTKVEFLKHTEHKNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCE 345
           +L+T+V++LKH E KNFA++DAAMNDL+RPA+Y+AW  +  ++   G+ + YD+VGPVCE
Sbjct: 300 LLLTEVQYLKHGEGKNFAVVDAAMNDLMRPAMYEAWHGVKTVKENAGQPRIYDVVGPVCE 359

Query: 346 TSDFLGKDRDLVLQEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREEL 405
           + D+L + R+L + EGDLLA+ S+GAYG TM+SNYNTR R AEV+VDG + +L+R RE  
Sbjct: 360 SGDWLARSRELAIGEGDLLALMSAGAYGMTMASNYNTRGRAAEVLVDGERAHLIRARENP 419

Query: 406 SSLWALESVL 415
           + L+ALE ++
Sbjct: 420 ADLFALEKIV 429


Lambda     K      H
   0.319    0.137    0.405 

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: 499
Number of extensions: 29
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: 417
Length of database: 430
Length adjustment: 32
Effective length of query: 385
Effective length of database: 398
Effective search space:   153230
Effective search space used:   153230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate HSERO_RS00950 HSERO_RS00950 (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.17098.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   6.5e-158  511.5   0.0   8.1e-158  511.2   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS00950  HSERO_RS00950 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS00950  HSERO_RS00950 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.2   0.0  8.1e-158  8.1e-158       5     416 ..       7     426 ..       4     427 .. 0.95

  Alignments for each domain:
  == domain 1  score: 511.2 bits;  conditional E-value: 8.1e-158
                                  TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka...ees......lvlYAvKAnsnl 63 
                                                ++g l +e+v+l++lae+fgtPlYvy++++l e+++a+++a ++   +        lv+Y vK+nsnl
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950   7 RNGVLHAEQVSLATLAEQFGTPLYVYSKAALVENFSAYANACQQagrA-DggkggaLVCYSVKSNSNL 73 
                                                7899**********************************9999875541.13445679*********** PP

                                  TIGR01048  64 avlrllaeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelell 131
                                                avl+ll ++G+g+d+vsgGEl r++aAg +a k++fsg+gk ++e++ ale++i ++nv+s+ e+++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950  74 AVLNLLGRLGSGFDIVSGGELLRVVAAGGDARKVIFSGVGKGRDEMKLALEHDILCFNVESIPEVARL 141
                                                ******************************************************************** PP

                                  TIGR01048 132 eeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIG 199
                                                +e+a+ lgk+ar++lRvnp+vdakth+yisTGlke+KFG+++e+a++ y++a++l+++e+vGi++HIG
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 142 NEVAGALGKRARISLRVNPNVDAKTHPYISTGLKENKFGVAYEDALNCYRAAAALPHIEVVGIDCHIG 209
                                                ******************************************************************** PP

                                  TIGR01048 200 SqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea. 266
                                                Sq+ld +p+ ea++k++++++ l++egi +++ld+GGG+gi+y++e+ ++ + +y + + +++     
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 210 SQLLDDSPLLEALDKIIDMVDALEAEGIPIHHLDIGGGIGIRYDDEQ-PVAIGDYLARVFARVDAWRa 276
                                                ********************************************999.*******9999998876433 PP

                                  TIGR01048 267 ..elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrl 332
                                                   +g+  ++++EpGRs+v+nag llt+V+++K+ e ++f++vDa+mndl+Rpa+Yea+h + ++k+ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 277 skYQGRPIQVMFEPGRSVVGNAGLLLTEVQYLKHGEGKNFAVVDAAMNDLMRPAMYEAWHGVKTVKE- 343
                                                3356779**********************************************************66. PP

                                  TIGR01048 333 eeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegka 400
                                                ++ +   +dvvGp+CEsgD la+ rel   e Gdlla++saGAYg++m+snYn+r+r+aevlv++++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 344 NAGQPRIYDVVGPVCESGDWLARSRELAIGE-GDLLALMSAGAYGMTMASNYNTRGRAAEVLVDGERA 410
                                                88889**********************9888.************************************ PP

                                  TIGR01048 401 rlirrretledllale 416
                                                +lir re+ +dl+ale
  lcl|FitnessBrowser__HerbieS:HSERO_RS00950 411 HLIRARENPADLFALE 426
                                                *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (430 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: 8.11
//
[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