Alignments for a candidate for dapC in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Xenophilus azovorans DSM 13620

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_038217081.1 Q392_RS28975 succinyldiaminopimelate transaminase

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



>NCBI__GCF_000745855.1:WP_038217081.1
          Length = 403

 Score =  459 bits (1182), Expect = e-134
 Identities = 243/401 (60%), Positives = 286/401 (71%), Gaps = 10/401 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP L  L PYPFE+LR L A   +P     PI+L IGEP+H  P  +  A+   L  L+
Sbjct: 1   MNPLLAKLQPYPFERLRQLFAGV-QPDPAHTPISLGIGEPRHPTPPFIKDALVEGLGALA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDP--SAGA 118
           +YP+T G+  LRQA + WL RRY++   DP ++VLPV GSREALFA AQTV+D   S   
Sbjct: 60  IYPATAGDLKLRQAFTGWLKRRYALEV-DPATQVLPVNGSREALFALAQTVVDATRSPAP 118

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           +V+ PNPFYQIYEGAALLAGA  +Y  +DPAR+F +    VP EVW RTQLV+VCSPGNP
Sbjct: 119 VVISPNPFYQIYEGAALLAGADTWYAPSDPARNFAVDWDSVPAEVWARTQLVYVCSPGNP 178

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G VM L EW  LF LSDRHGFVIA+ ECYSEIY   D PPLG L+AA +LGR  + NL+
Sbjct: 179 TGAVMPLAEWEKLFALSDRHGFVIASDECYSEIYF-RDEPPLGGLEAAAKLGRGDFRNLI 237

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMRRMCR 297
           A +SLSKRSNVPG+RSGFVAGDAA++ +FLLYRTYHGSAMS  V+AASIAAW     +  
Sbjct: 238 ALTSLSKRSNVPGLRSGFVAGDAAIVRQFLLYRTYHGSAMSGAVAAASIAAWGDESHVVD 297

Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTP----GSDTAFARELYGRTGVTVLP 353
              QYR KF AV P+L+ VLDVR P ASFYLWAG P    G D AFAR LY +  VTVLP
Sbjct: 298 NRMQYRTKFAAVTPMLEAVLDVRLPDASFYLWAGIPPGWNGDDAAFARALYAQYNVTVLP 357

Query: 354 GSLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           GS LARE+  ANPG+GRIR+ALVA   +C +AA RI  F R
Sbjct: 358 GSYLARESQGANPGRGRIRMALVADTPECTEAARRIVDFTR 398


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: 602
Number of extensions: 30
Number of successful extensions: 7
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: 403
Length adjustment: 31
Effective length of query: 366
Effective length of database: 372
Effective search space:   136152
Effective search space used:   136152
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_038217081.1 Q392_RS28975 (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.13230.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-183  595.6   0.0   2.4e-183  595.4   0.0    1.0  1  lcl|NCBI__GCF_000745855.1:WP_038217081.1  Q392_RS28975 succinyldiaminopime


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_038217081.1  Q392_RS28975 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  595.4   0.0  2.4e-183  2.4e-183       1     394 [.       1     396 [.       1     397 [. 0.98

  Alignments for each domain:
  == domain 1  score: 595.4 bits;  conditional E-value: 2.4e-183
                                 TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpe 69 
                                               mnp l++l+pyPfe+l++l+++v+p   + +i+l iGeP+h+tP f+++alve l +l+ yP+t+G+ +
  lcl|NCBI__GCF_000745855.1:WP_038217081.1   1 MNPLLAKLQPYPFERLRQLFAGVQPDPAHTPISLGIGEPRHPTPPFIKDALVEGLGALAIYPATAGDLK 69 
                                               9******************************************************************** PP

                                 TIGR03538  70 lreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidrae..kalvvlPnPfyqiyeGaall 136
                                               lr+a + Wl+rr++l+   dp++qvlPvnG+realfa++q+v+d ++  +++v++PnPfyqiyeGaall
  lcl|NCBI__GCF_000745855.1:WP_038217081.1  70 LRQAFTGWLKRRYALEV--DPATQVLPVNGSREALFALAQTVVDATRspAPVVISPNPFYQIYEGAALL 136
                                               **************986..*************************99977899***************** PP

                                 TIGR03538 137 agaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasd 205
                                               aga+ ++ +++++ +f  d+d+vp+evW+r+ql++vcsPgnPtGav++l e++kl++l+d+++f+iasd
  lcl|NCBI__GCF_000745855.1:WP_038217081.1 137 AGADTWYAPSDPARNFAVDWDSVPAEVWARTQLVYVCSPGNPTGAVMPLAEWEKLFALSDRHGFVIASD 205
                                               ********************************************************************* PP

                                 TIGR03538 206 ecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyh 274
                                               ecyse+y+  +e+P+G leaaa+lGr df++l++++slskrsnvPGlrsGfvaGda+++++fl yrtyh
  lcl|NCBI__GCF_000745855.1:WP_038217081.1 206 ECYSEIYF-RDEPPLGGLEAAAKLGRGDFRNLIALTSLSKRSNVPGLRSGFVAGDAAIVRQFLLYRTYH 273
                                               ********.556********************************************************* PP

                                 TIGR03538 275 GcampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPdasfylWlkv...pdgddea 340
                                               G+am+ av +asiaaW de+hv +nr +yr kfaav+ +l+avld++lPdasfylW+ +    +gdd+a
  lcl|NCBI__GCF_000745855.1:WP_038217081.1 274 GSAMSGAVAAASIAAWGDESHVVDNRMQYRTKFAAVTPMLEAVLDVRLPDASFYLWAGIppgWNGDDAA 342
                                               *********************************************************99433468**** PP

                                 TIGR03538 341 faralyeeenvkvlpGrylsreaegvnPGegrvrlalvaeleecveaaerikkl 394
                                               faraly++ nv+vlpG+yl+re++g+nPG+gr+r+alva++ ec+eaa+ri ++
  lcl|NCBI__GCF_000745855.1:WP_038217081.1 343 FARALYAQYNVTVLPGSYLARESQGANPGRGRIRMALVADTPECTEAARRIVDF 396
                                               ***************************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (403 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.82
//
[ok]

This GapMind analysis is from Apr 10 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