Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N1B4

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Pf1N1B4_3080 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080
          Length = 399

 Score =  412 bits (1059), Expect = e-120
 Identities = 217/395 (54%), Positives = 266/395 (67%), Gaps = 4/395 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L+ L PYPFEKLRALL     P  D   I LSIGEPKH +PA V +A+A+NL  ++
Sbjct: 1   MNNALNQLQPYPFEKLRALLGSV-TPNPDKRAIALSIGEPKHRSPAFVAEALASNLDQMA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYP+T G PALR+AI+ W  RR+S+P    DP   VLPV G+REALFAF QTV++    A
Sbjct: 60  VYPTTLGIPALREAIAAWCERRFSVPNGWLDPARNVLPVNGTREALFAFTQTVVNRGDDA 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 H FVIAA ECYSE+Y DE TPP G L A   LGR  +   V
Sbjct: 180 TGALIPVETLKKLIALADEHDFVIAADECYSELYFDEQTPPAGLLSACVELGRKDFKRCV 239

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

Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
             A YR K++AVL IL  V++V+ P   FYLW    G D AF R+L+ +  VTV+PGS L
Sbjct: 300 NRALYREKYDAVLEILSPVMEVQRPDGGFYLWPNVNGDDAAFCRDLFEQEHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +R+    NPG GRIR+ALVAPL +CV+AAERI  F
Sbjct: 360 SRDVDGVNPGAGRIRMALVAPLAECVEAAERIRAF 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: 507
Number of extensions: 28
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 Pf1N1B4_3080 (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.6896.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   5.9e-211  686.3   0.0   6.6e-211  686.1   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080  N-succinyl-L,L-diaminopimelate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080  N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.1   0.0  6.6e-211  6.6e-211       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 686.1 bits;  conditional E-value: 6.6e-211
                                      TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPtt 64 
                                                    mn++l++l+pyPfekl++ll +vtp+ d+++ialsiGePkh++Pafv+eal++nl++++ yPtt
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080   1 MNNALNQLQPYPFEKLRALLGSVTPNPDKRAIALSIGEPKHRSPAFVAEALASNLDQMAVYPTT 64 
                                                    9*************************************************************** PP

                                      TIGR03538  65 kGlpelreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfy 127
                                                     G+p+lreaia+W+errf++p+g +dp+r+vlPvnGtrealfaf+q+v++r ++alvv+PnPfy
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080  65 LGIPALREAIAAWCERRFSVPNGwLDPARNVLPVNGTREALFAFTQTVVNRGDDALVVSPNPFY 128
                                                    **************************************************************** PP

                                      TIGR03538 128 qiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkkl 191
                                                    qiyeGaa+laga+p++l+c +engf+pdfdav+ ++Wkr+q+lf+csPgnPtGa++++e+lkkl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080 129 QIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIWKRCQILFLCSPGNPTGALIPVETLKKL 192
                                                    **************************************************************** PP

                                      TIGR03538 192 leladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsG 255
                                                    ++lad++df+ia+decysely+de+++P+Gll+a+ elGr+dfkr++vfhslskrsn+PGlrsG
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080 193 IALADEHDFVIAADECYSELYFDEQTPPAGLLSACVELGRKDFKRCVVFHSLSKRSNLPGLRSG 256
                                                    **************************************************************** PP

                                      TIGR03538 256 fvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaavleilgavld 319
                                                    fvaGda++lk fl yrtyhGcamp+++qlas+aaW+de hvr+nralyrek++avleil++v++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080 257 FVAGDADILKGFLLYRTYHGCAMPVQTQLASVAAWNDEVHVRANRALYREKYDAVLEILSPVME 320
                                                    **************************************************************** PP

                                      TIGR03538 320 lelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaelee 383
                                                    +++Pd++fylW++v +gdd+af+r+l+e+e+v+v+pG+ylsr+++gvnPG+gr+r+alva+l+e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080 321 VQRPDGGFYLWPNV-NGDDAAFCRDLFEQEHVTVVPGSYLSRDVDGVNPGAGRIRMALVAPLAE 383
                                                    **************.8************************************************ PP

                                      TIGR03538 384 cveaaerikkll 395
                                                    cveaaeri++++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3080 384 CVEAAERIRAFI 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.26
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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