GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Pseudomonas fluorescens FW300-N2C3

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate AO356_06055 AO356_06055 succinyldiaminopimelate transaminase

Query= BRENDA::Q9ZEX3
         (397 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 AO356_06055
           succinyldiaminopimelate transaminase
          Length = 399

 Score =  417 bits (1071), Expect = e-121
 Identities = 219/395 (55%), Positives = 268/395 (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  VYPTTLGIPELREAITGWCERRFNVPTGWLDPARHVLPVNGTREALFAFTQTVVNRGDDA 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAA LAGA P+Y+    A  F      V  ++W+R Q++F+CSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNP 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
           +R+    NPG GR+R+ALVAPL +CV+AAERI  F
Sbjct: 360 SRDVDGVNPGAGRVRMALVAPLAECVEAAERIRAF 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: 506
Number of extensions: 25
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 AO356_06055 AO356_06055 (succinyldiaminopimelate transaminase)
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.29150.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.6e-211  687.4   0.0     3e-211  687.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055  AO356_06055 succinyldiaminopimel


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055  AO356_06055 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.3   0.0    3e-211    3e-211       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 687.3 bits;  conditional E-value: 3e-211
                                       TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPt 63 
                                                     mn++l++l+pyPfekl++ll +vtp+ d+++ialsiGePkh++P+fv+eal++nle+++ yPt
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055   1 MNNALNQLQPYPFEKLRALLGSVTPNPDKRPIALSIGEPKHRSPSFVAEALASNLEKMAVYPT 63 
                                                     9************************************************************** PP

                                       TIGR03538  64 tkGlpelreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnP 125
                                                     t G+pelreai+ W+errf++p+g +dp+r+vlPvnGtrealfaf+q+v++r ++alvv+PnP
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055  64 TLGIPELREAITGWCERRFNVPTGwLDPARHVLPVNGTREALFAFTQTVVNRGDDALVVSPNP 126
                                                     *************************************************************** PP

                                       TIGR03538 126 fyqiyeGaallagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleel 188
                                                     fyqiyeGaa+laga+p++l+c ++ngf+pdfdav+ ++Wkr+q+lf+csPgnPtGa+++++ l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 127 FYQIYEGAAFLAGAKPHYLPCLDANGFNPDFDAVSPDIWKRCQILFLCSPGNPTGALIPVDVL 189
                                                     *************************************************************** PP

                                       TIGR03538 189 kklleladkydfiiasdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPG 251
                                                     kkl++lad++df+ia+decysely+de+++P Gll+a+ elGr+dfkr++vfhslskrsn+PG
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 190 KKLIALADEHDFVIAADECYSELYFDEQTPPPGLLSACVELGRKDFKRCVVFHSLSKRSNLPG 252
                                                     *************************************************************** PP

                                       TIGR03538 252 lrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvrenralyrekfaavleil 314
                                                     lrsGfvaGda++lk fl yrtyhGcamp+++qlasiaaW+de hvr+nralyrekf+avleil
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 253 LRSGFVAGDADILKGFLLYRTYHGCAMPVQTQLASIAAWNDEVHVRANRALYREKFDAVLEIL 315
                                                     *************************************************************** PP

                                       TIGR03538 315 gavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlal 377
                                                     ++vld+++Pd+sfylW++v  gdd+af+r+l+e+e+v+v+pG+ylsr+++gvnPG+grvr+al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 316 SPVLDVQRPDGSFYLWPNV-AGDDAAFCRDLFEQEHVTVVPGSYLSRDVDGVNPGAGRVRMAL 377
                                                     *******************.7****************************************** PP

                                       TIGR03538 378 vaeleecveaaerikkll 395
                                                     va+l+ecveaaeri++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_06055 378 VAPLAECVEAAERIRAFI 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.14
//
[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:

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 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