Alignments for a candidate for dapC in Methylomonas methanica MC09

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Methylomonas methanica MC09

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_013820662.1 METME_RS20555 succinyldiaminopimelate transaminase

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



>NCBI__GCF_000214665.1:WP_013820662.1
          Length = 400

 Score =  409 bits (1052), Expect = e-119
 Identities = 211/395 (53%), Positives = 267/395 (67%), Gaps = 4/395 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP L  LHPYPFEKL  L      P H    I LSIGEPKHA PA + +A+  +L GL+
Sbjct: 1   MNPHLQLLHPYPFEKLAELKQGITPPAHKAH-IALSIGEPKHATPAFIQEALVRHLQGLT 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
            YP+TKG P LRQAI+ W+ RR++IPA   D +++V+PV G+REALFA  Q V+DP    
Sbjct: 60  QYPTTKGLPELRQAIADWIGRRFAIPAEHIDADTQVMPVNGTREALFAIVQAVVDPREKP 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           +V+ PNPFYQIYEGAALLAGA PYY+N   A  +      VP+ +W+R QL+F+CSPGNP
Sbjct: 120 VVIMPNPFYQIYEGAALLAGAEPYYLNTLEADGYLPDFNSVPEAIWQRCQLIFICSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G VMS  +   L EL+ R+ FVIA+ ECY+E+Y DE  PP G LQ+A + G   + N V
Sbjct: 180 TGTVMSQADHEKLLELATRYNFVIASDECYTELYDDEALPPRGLLQSAYQAGMIDFKNCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298
            F SLSKRSN PG+RSGFVAGDA +L +FL YRTYHG  M      ASIAAW      ++
Sbjct: 240 IFQSLSKRSNAPGLRSGFVAGDAEILRQFLKYRTYHGCPMPVTTQHASIAAWRDEAHVQQ 299

Query: 299 TAQ-YRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
             Q YR KF A + ILQ+V ++  P ASFY+W  T   DT FA +L+ +  +TVLPGS L
Sbjct: 300 NRQLYRDKFTAFIEILQDVCEISRPPASFYIWLKTALPDTEFALQLFAQQNITVLPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +R++   NPG   +RIALVAPL++CV+AA+RI  F
Sbjct: 360 SRDSGGINPGANHVRIALVAPLEECVEAAQRIKAF 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: 508
Number of extensions: 22
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: 400
Length adjustment: 31
Effective length of query: 366
Effective length of database: 369
Effective search space:   135054
Effective search space used:   135054
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 WP_013820662.1 METME_RS20555 (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.3243375.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-200  651.9   0.0   1.9e-200  651.7   0.0    1.0  1  NCBI__GCF_000214665.1:WP_013820662.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000214665.1:WP_013820662.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.7   0.0  1.9e-200  1.9e-200       1     395 []       1     395 [.       1     395 [. 1.00

  Alignments for each domain:
  == domain 1  score: 651.7 bits;  conditional E-value: 1.9e-200
                             TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpelrea 73 
                                           mnp+l+ l+pyPfeklael++++tppa++ +ialsiGePkhatPaf++ealv++l++l++yPttkGlpelr+a
  NCBI__GCF_000214665.1:WP_013820662.1   1 MNPHLQLLHPYPFEKLAELKQGITPPAHKAHIALSIGEPKHATPAFIQEALVRHLQGLTQYPTTKGLPELRQA 73 
                                           9************************************************************************ PP

                             TIGR03538  74 iaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaallagaepyfln 145
                                           ia+W+ rrf++pa  +d+++qv+PvnGtrealfa+vqav+d++ek++v++PnPfyqiyeGaallagaepy+ln
  NCBI__GCF_000214665.1:WP_013820662.1  74 IADWIGRRFAIPAEhIDADTQVMPVNGTREALFAIVQAVVDPREKPVVIMPNPFYQIYEGAALLAGAEPYYLN 146
                                           ************999********************************************************** PP

                             TIGR03538 146 ctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasdecyselyldeaea 218
                                           + +++g+ pdf++vpe +W+r+ql+f+csPgnPtG+v+s+ + +kllela +y+f+iasdecy+ely dea +
  NCBI__GCF_000214665.1:WP_013820662.1 147 TLEADGYLPDFNSVPEAIWQRCQLIFICSPGNPTGTVMSQADHEKLLELATRYNFVIASDECYTELYDDEALP 219
                                           ************************************************************************* PP

                             TIGR03538 219 PvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhGcampiavqlasiaaWe 291
                                           P Gll++a + G  dfk++++f+slskrsn+PGlrsGfvaGdae+l++fl+yrtyhGc mp+++q+asiaaW 
  NCBI__GCF_000214665.1:WP_013820662.1 220 PRGLLQSAYQAGMIDFKNCVIFQSLSKRSNAPGLRSGFVAGDAEILRQFLKYRTYHGCPMPVTTQHASIAAWR 292
                                           ************************************************************************* PP

                             TIGR03538 292 dekhvrenralyrekfaavleilgavldlelPdasfylWlkvpdgddeafaralyeeenvkvlpGrylsreae 364
                                           de+hv++nr+lyr+kf a++eil++v ++++P asfy+Wlk+   +d++fa +l++++n++vlpG+ylsr++ 
  NCBI__GCF_000214665.1:WP_013820662.1 293 DEAHVQQNRQLYRDKFTAFIEILQDVCEISRPPASFYIWLKT-ALPDTEFALQLFAQQNITVLPGSYLSRDSG 364
                                           ******************************************.7***************************** PP

                             TIGR03538 365 gvnPGegrvrlalvaeleecveaaerikkll 395
                                           g nPG+++vr+alva+leecveaa+rik+++
  NCBI__GCF_000214665.1:WP_013820662.1 365 GINPGANHVRIALVAPLEECVEAAQRIKAFI 395
                                           ****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (400 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.34
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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