Alignments for a candidate for dapC in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudomonas fluorescens GW456-L13

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate PfGW456L13_4713 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

Query= metacyc::MONOMER-6501
         (397 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713
          Length = 399

 Score =  413 bits (1062), Expect = e-120
 Identities = 217/395 (54%), Positives = 264/395 (66%), Gaps = 4/395 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L  L PYPFEKLRALL     P  D  PI LSIGEPKH +P+ V +A+A NL  ++
Sbjct: 1   MNNALSQLQPYPFEKLRALLGSV-TPNPDKRPIALSIGEPKHRSPSFVAEALAGNLEKMA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYP+T G P LR+AI+ W  RR+ +P    DP   VLPV G+REALFAF QTV++    A
Sbjct: 60  VYPTTLGIPELREAIAAWCERRFDVPKGWIDPARNVLPVNGTREALFAFTQTVVNRGDDA 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAA LAGA P+Y+       F      V  ++W+R Q++F+CSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIWKRCQILFLCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G ++ +E  + L  L+D + FVIAA ECYSE+Y DE TPP G L A   LGR  +   V
Sbjct: 180 TGALIPVETLKKLIALADEYDFVIAADECYSELYFDEQTPPPGLLSACAELGRKDFKRCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCR- 297
            F SLSKRSN+PG+RSGFVAGDA +L  FLLYRTYHG AM      AS+AAW+     R 
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDADVLKGFLLYRTYHGCAMPVQTQLASVAAWNDEVHVRA 299

Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
             A YR KF+AVL IL  VLDV+ P  SFYLW    G D AF R+L+ +  VTV+PGS L
Sbjct: 300 NRALYREKFDAVLEILSPVLDVQRPDGSFYLWPNVAGDDAAFCRDLFEQEHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +R+    NPG GR+R+ALVAPL +CV+AAERI  F
Sbjct: 360 SRDVDGVNPGAGRVRMALVAPLAECVEAAERIRDF 394


Lambda     K      H
   0.321    0.135    0.412 

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: 512
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate PfGW456L13_4713 (N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17))
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03538.hmm
# target sequence database:        /tmp/gapView.7868.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03538  [M=395]
Accession:   TIGR03538
Description: DapC_gpp: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.3e-212  691.7   0.0   1.5e-212  691.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713  N-succinyl-L,L-diaminopimelate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713  N-succinyl-L,L-diaminopimelate aminotransferase alternative (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  691.6   0.0  1.5e-212  1.5e-212       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 691.6 bits;  conditional E-value: 1.5e-212
                                               TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenl 55 
                                                             mn++l++l+pyPfekl++ll +vtp+ d+++ialsiGePkh++P+fv+eal+ nl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713   1 MNNALSQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALAGNL 55 
                                                             9****************************************************** PP

                                               TIGR03538  56 eelskyPttkGlpelreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvq 109
                                                             e+++ yPtt G+pelreaia+W+errf++p+g +dp+r+vlPvnGtrealfaf+q
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713  56 EKMAVYPTTLGIPELREAIAAWCERRFDVPKGwIDPARNVLPVNGTREALFAFTQ 110
                                                             ******************************************************* PP

                                               TIGR03538 110 avidraekalvvlPnPfyqiyeGaallagaepyflnctaengfkpdfdavpeevW 164
                                                             +v++r ++alvv+PnPfyqiyeGaa+laga+p++l+c +engf+pdfdav+ ++W
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 111 TVVNRGDDALVVSPNPFYQIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIW 165
                                                             ******************************************************* PP

                                               TIGR03538 165 krvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaP 219
                                                             kr+q+lf+csPgnPtGa++++e+lkkl++lad+ydf+ia+decysely+de+++P
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 166 KRCQILFLCSPGNPTGALIPVETLKKLIALADEYDFVIAADECYSELYFDEQTPP 220
                                                             ******************************************************* PP

                                               TIGR03538 220 vGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyh 274
                                                              Gll+a+aelGr+dfkr++vfhslskrsn+PGlrsGfvaGda++lk fl yrtyh
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 221 PGLLSACAELGRKDFKRCVVFHSLSKRSNLPGLRSGFVAGDADVLKGFLLYRTYH 275
                                                             ******************************************************* PP

                                               TIGR03538 275 GcampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPdasfyl 329
                                                             Gcamp+++qlas+aaW+de hvr+nralyrekf+avleil++vld+++Pd+sfyl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 276 GCAMPVQTQLASVAAWNDEVHVRANRALYREKFDAVLEILSPVLDVQRPDGSFYL 330
                                                             ******************************************************* PP

                                               TIGR03538 330 WlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaeleec 384
                                                             W++v  gdd+af+r+l+e+e+v+v+pG+ylsr+++gvnPG+grvr+alva+l+ec
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 331 WPNV-AGDDAAFCRDLFEQEHVTVVPGSYLSRDVDGVNPGAGRVRMALVAPLAEC 384
                                                             ****.7************************************************* PP

                                               TIGR03538 385 veaaerikkll 395
                                                             veaaeri++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713 385 VEAAERIRDFI 395
                                                             ********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (399 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: 00:00:00.01
# Mc/sec: 12.14
//
[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