Alignments for a candidate for dapC in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudomonas putida KT2440

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate PP_1588 PP_1588 N-succinyl-L,L-diaminopimelate aminotransferase alternative

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



>FitnessBrowser__Putida:PP_1588
          Length = 398

 Score =  432 bits (1112), Expect = e-126
 Identities = 227/395 (57%), Positives = 269/395 (68%), Gaps = 4/395 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L  L PYPFEKLRALL    KP  D   I LSIGEPKH +PA V QA+A NL  L+
Sbjct: 1   MNHALTQLQPYPFEKLRALLGSV-KPAADKRAIALSIGEPKHESPAFVAQAMADNLDKLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYPST G PALRQAI QW  RR+ +PA   D +  +LPV G+REALFAF Q V++ +   
Sbjct: 60  VYPSTLGLPALRQAIGQWCERRFGVPAGWLDADRHILPVNGTREALFAFTQAVVNRADDG 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LV+ PNPFYQIYEGAALLAGATP+Y+       F      VP EVW+R Q++F+CSPGNP
Sbjct: 120 LVISPNPFYQIYEGAALLAGATPHYLPCLENNGFNPDFDAVPAEVWKRCQILFLCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G ++ +   + L  L+D H FVIAA ECYSE+Y DED PP G L A   LGR  +   V
Sbjct: 180 TGALVPMNTLKKLIALADEHDFVIAADECYSELYFDEDAPPPGLLSACAELGRSDFARCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298
            F SLSKRSN+PG+RSGFVAGDA ++  FLLYRTYHG AM      ASIAAW      R+
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDAQIIKPFLLYRTYHGCAMPVQTQLASIAAWQDEAHVRE 299

Query: 299 TA-QYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
              QYRAK++AVL ILQ VLDV+ P  SFYLWA  PG D  F R+L+    VTV+PGS L
Sbjct: 300 NRDQYRAKYDAVLDILQPVLDVQRPDGSFYLWAKVPGDDAEFTRDLFEAQHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +RE    NPG GR+R+ALVAPL +C++AAERI  F
Sbjct: 360 SREVDGVNPGAGRVRMALVAPLAECIEAAERIRAF 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: 540
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: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 PP_1588 PP_1588 (N-succinyl-L,L-diaminopimelate aminotransferase alternative)
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.25382.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-208  678.9   0.0   1.2e-208  678.7   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1588  PP_1588 N-succinyl-L,L-diaminopi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1588  PP_1588 N-succinyl-L,L-diaminopimelate aminotransferase alternative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.7   0.0  1.2e-208  1.2e-208       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 678.7 bits;  conditional E-value: 1.2e-208
                           TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelreaia 75 
                                         mn++l++l+pyPfekl++ll +v+p+ad+++ialsiGePkh +Pafv++a+++nl++l+ yP+t Glp+lr+ai 
  lcl|FitnessBrowser__Putida:PP_1588   1 MNHALTQLQPYPFEKLRALLGSVKPAADKRAIALSIGEPKHESPAFVAQAMADNLDKLAVYPSTLGLPALRQAIG 75 
                                         9************************************************************************** PP

                           TIGR03538  76 eWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallagaepyflnctae 149
                                         +W+errf +pag +d++r++lPvnGtrealfaf+qav++ra++ lv++PnPfyqiyeGaallaga+p++l+c ++
  lcl|FitnessBrowser__Putida:PP_1588  76 QWCERRFGVPAGwLDADRHILPVNGTREALFAFTQAVVNRADDGLVISPNPFYQIYEGAALLAGATPHYLPCLEN 150
                                         *************************************************************************** PP

                           TIGR03538 150 ngfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaeaPvGlle 224
                                         ngf+pdfdavp+evWkr+q+lf+csPgnPtGa++++++lkkl++lad++df+ia+decysely+de+++P Gll+
  lcl|FitnessBrowser__Putida:PP_1588 151 NGFNPDFDAVPAEVWKRCQILFLCSPGNPTGALVPMNTLKKLIALADEHDFVIAADECYSELYFDEDAPPPGLLS 225
                                         *************************************************************************** PP

                           TIGR03538 225 aaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWedekhvren 299
                                         a+aelGr+df r++vfhslskrsn+PGlrsGfvaGda+++k fl yrtyhGcamp+++qlasiaaW+de+hvren
  lcl|FitnessBrowser__Putida:PP_1588 226 ACAELGRSDFARCVVFHSLSKRSNLPGLRSGFVAGDAQIIKPFLLYRTYHGCAMPVQTQLASIAAWQDEAHVREN 300
                                         *************************************************************************** PP

                           TIGR03538 300 ralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreaegvnPGegrvr 374
                                         r++yr+k++avl+il++vld+++Pd+sfylW+kv +gdd++f+r+l+e+++v+v+pG+ylsre++gvnPG+grvr
  lcl|FitnessBrowser__Putida:PP_1588 301 RDQYRAKYDAVLDILQPVLDVQRPDGSFYLWAKV-PGDDAEFTRDLFEAQHVTVVPGSYLSREVDGVNPGAGRVR 374
                                         **********************************.5*************************************** PP

                           TIGR03538 375 lalvaeleecveaaerikkll 395
                                         +alva+l+ec+eaaeri+++l
  lcl|FitnessBrowser__Putida:PP_1588 375 MALVAPLAECIEAAERIRAFL 395
                                         ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (398 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: 11.17
//
[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