GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2E2

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate Pf6N2E2_3073 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073
          Length = 399

 Score =  415 bits (1067), Expect = e-120
 Identities = 219/395 (55%), Positives = 267/395 (67%), Gaps = 4/395 (1%)

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

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

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCR- 297
            F SLSKRSN+PG+RSGFVAGDA +L  FLLYRTYHG AM      ASIAAW+     R 
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRA 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
           +RE    NPG GR+R+ALVAPL +CV+AAERI  F
Sbjct: 360 SREVDGVNPGAGRVRMALVAPLAECVEAAERIRAF 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: 511
Number of extensions: 26
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 Pf6N2E2_3073 (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.5994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-211  688.7   0.0   1.2e-211  688.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073  N-succinyl-L,L-diaminopimelate a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073  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 !  688.6   0.0  1.2e-211  1.2e-211       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 688.6 bits;  conditional E-value: 1.2e-211
                                      TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPtt 64 
                                                    mn++l++l+pyPfekl++ll +vtp+ d+++ialsiGePkh++P+fv+eal++nle+++ yPtt
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073   1 MNNALNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAVYPTT 64 
                                                    9*************************************************************** PP

                                      TIGR03538  65 kGlpelreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfy 127
                                                     G+pelreai+ W+errf++p+g +dp+r+vlPvnGtrealfaf+q+v++r ++alvv+PnPfy
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073  65 LGIPELREAITGWCERRFNVPNGwLDPARHVLPVNGTREALFAFTQTVVNRGDDALVVSPNPFY 128
                                                    **************************************************************** PP

                                      TIGR03538 128 qiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkkl 191
                                                    qiyeGaa+laga+p++l+c +engf+pdfdav+ ++Wkr+q+lf+csPgnPtGa+++++ lkkl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073 129 QIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSPDIWKRCQILFLCSPGNPTGALIPVDVLKKL 192
                                                    **************************************************************** PP

                                      TIGR03538 192 leladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsG 255
                                                    ++lad++df+ia+decysely+de+++P Gll+a+ elGr+dfkr++vfhslskrsn+PGlrsG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073 193 IALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCVVFHSLSKRSNLPGLRSG 256
                                                    **************************************************************** PP

                                      TIGR03538 256 fvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaavleilgavld 319
                                                    fvaGda++lk fl yrtyhGcamp+++qlasiaaW+de hvr+nralyrekf+avleil++vld
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073 257 FVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRANRALYREKFDAVLEILSPVLD 320
                                                    **************************************************************** PP

                                      TIGR03538 320 lelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaelee 383
                                                    +++Pd+sfylW++v  gdd+af+r+l+e+e+v+v+pG+ylsre++gvnPG+grvr+alva+l+e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073 321 VQRPDGSFYLWPNV-AGDDAAFCRDLFEQEHVTVVPGSYLSREVDGVNPGAGRVRMALVAPLAE 383
                                                    **************.7************************************************ PP

                                      TIGR03538 384 cveaaerikkll 395
                                                    cveaaeri++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3073 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.18
//
[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:

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:

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:

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:

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