Alignments for a candidate for lysA in Hyphomicrobium sulfonivorans WDL6

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Hyphomicrobium sulfonivorans WDL6

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_068461975.1 APY04_RS09415 diaminopimelate decarboxylase

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



>NCBI__GCF_001541235.1:WP_068461975.1
          Length = 422

 Score =  415 bits (1067), Expect = e-120
 Identities = 218/422 (51%), Positives = 283/422 (67%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           M HF  ++GVLHAE VS+  IA EVGTP Y YSTATLERH   L  A AG  ++ + FA+
Sbjct: 1   MHHFEYRDGVLHAEGVSLARIAEEVGTPFYCYSTATLERHYRVLTEAFAGQDAL-ICFAV 59

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           KAN N AVL  LAR G G DVVS GEL+RALA G+PA  ++F+GVGKTR+E+   L+ GI
Sbjct: 60  KANSNQAVLATLARLGAGMDVVSEGELRRALAVGVPASRIIFAGVGKTRSEMAFALEAGI 119

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
             FN+E E E   L+++A A GKTA   LRVNPDVDA THAKISTGKAENKFG+   +A 
Sbjct: 120 LGFNVESEPELRALSEVASALGKTAHVALRVNPDVDAKTHAKISTGKAENKFGIPYAQAR 179

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
           +++   A  PG+   G+ +HIGSQ+T+L P   A++ + E+V QL A GH + H+D+GGG
Sbjct: 180 QLYAEAASLPGIAATGIHMHIGSQITQLDPFRNAFRLMREMVEQLIADGHKLQHLDIGGG 239

Query: 241 LGVPY-HAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299
           LGVPY   G+       +  +V     G  + ++ EPGR I GNAGVLVT+V++ K    
Sbjct: 240 LGVPYVSEGEVTPPPSAYAQIVREELAGLGLKIVMEPGRVIAGNAGVLVTQVVYCKEGVD 299

Query: 300 NPYVIVDAAMNDLARPALYDAYHEFEAVEP---TGEKFVANIAGPVCETGDTFAMGREID 356
             + +VDAAMNDL RP LY+A HE   VE    +    V +I GPVCETGD  A+ R++ 
Sbjct: 300 KTFTVVDAAMNDLIRPTLYEALHEIWPVEEDKLSMPPVVQDIVGPVCETGDYLALDRKLP 359

Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416
            + SGDL    TAGAYGA M+S+YN+R LVPEVLV GD +AVV  R   E ++G +++P+
Sbjct: 360 PLSSGDLIAVMTAGAYGAVMSSSYNTRPLVPEVLVHGDAYAVVRPRFGIEQLIGLDKLPD 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: 534
Number of extensions: 27
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: 422
Length adjustment: 32
Effective length of query: 387
Effective length of database: 390
Effective search space:   150930
Effective search space used:   150930
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_068461975.1 APY04_RS09415 (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.15776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-148  479.9   0.0     3e-148  479.7   0.0    1.0  1  lcl|NCBI__GCF_001541235.1:WP_068461975.1  APY04_RS09415 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001541235.1:WP_068461975.1  APY04_RS09415 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.7   0.0    3e-148    3e-148       4     415 ..       6     414 ..       3     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 479.7 bits;  conditional E-value: 3e-148
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaee 72 
                                                +dg l +egv+l+++aee gtP+Y y+++tl+++++ l+eaf+++++l+++AvKAnsn avl +la++
  lcl|NCBI__GCF_001541235.1:WP_068461975.1   6 YRDGVLHAEGVSLARIAEEVGTPFYCYSTATLERHYRVLTEAFAGQDALICFAVKANSNQAVLATLARL 74 
                                               57899*****************************************9********************** PP

                                 TIGR01048  73 GlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkk 141
                                               G+g+dvvs+GEl rala gv+a++i+f+g+gk+++e++ ale++i  +nv+s+ el+ l+e+a  lgk+
  lcl|NCBI__GCF_001541235.1:WP_068461975.1  75 GAGMDVVSEGELRRALAVGVPASRIIFAGVGKTRSEMAFALEAGILGFNVESEPELRALSEVASALGKT 143
                                               ********************************************************************* PP

                                 TIGR01048 142 arvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfve 210
                                               a+v+lRvnpdvdakth +isTG++e+KFGi +++a++ y  a++l+ +  +Gih+HIGSqi++l+pf++
  lcl|NCBI__GCF_001541235.1:WP_068461975.1 144 AHVALRVNPDVDAKTHAKISTGKAENKFGIPYAQARQLYAEAASLPGIAATGIHMHIGSQITQLDPFRN 212
                                               ********************************************************************* PP

                                 TIGR01048 211 aaekvvklleelkeegieleeldlGGGlgisyeeeee.apdleeyaeklleklekeaelglklklilEp 278
                                               a++ + +++e+l ++g +l++ld+GGGlg++y +e e +p ++ ya+ + e+l++     l lk+++Ep
  lcl|NCBI__GCF_001541235.1:WP_068461975.1 213 AFRLMREMVEQLIADGHKLQHLDIGGGLGVPYVSEGEvTPPPSAYAQIVREELAG-----LGLKIVMEP 276
                                               ********************************88765268889999999999988.....89******* PP

                                 TIGR01048 279 GRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr.leeeetetvdvvGpl 346
                                               GR +++nagvl+t+V + Ke   ++f +vDa+mndliRp lYea hei ++++     + ++ d+vGp+
  lcl|NCBI__GCF_001541235.1:WP_068461975.1 277 GRVIAGNAGVLVTQVVYCKEGVDKTFTVVDAAMNDLIRPTLYEALHEIWPVEEdKLSMPPVVQDIVGPV 345
                                               ***************************************************88466788999******* PP

                                 TIGR01048 347 CEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllal 415
                                               CE+gD la dr+lp   +Gdl+av+ aGAYga mss Yn+rp + evlv+++ + ++r r  +e+l+ l
  lcl|NCBI__GCF_001541235.1:WP_068461975.1 346 CETGDYLALDRKLPPLSSGDLIAVMTAGAYGAVMSSSYNTRPLVPEVLVHGDAYAVVRPRFGIEQLIGL 414
                                               ************************************************************999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (422 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: 8.50
//
[ok]

This GapMind analysis is from Apr 10 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