Alignments for a candidate for dapC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Cupriavidus basilensis 4G11

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate RR42_RS11930 RR42_RS11930 succinyldiaminopimelate aminotransferase

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



>FitnessBrowser__Cup4G11:RR42_RS11930
          Length = 405

 Score =  468 bits (1203), Expect = e-136
 Identities = 245/404 (60%), Positives = 287/404 (71%), Gaps = 10/404 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNPRLD L PYPFEKLR LLAD  KP   LP I+  IGEPKH  P  +  A++  L GL+
Sbjct: 1   MNPRLDLLQPYPFEKLRVLLADV-KPNGALPAISFGIGEPKHPTPEFIKTALSNALQGLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSA-GAL 119
            YP+T G  ALRQ ++ W+ RRY++PA +  ++VLPV GSREALFAFAQTV+D S  GAL
Sbjct: 60  NYPTTAGSDALRQCMAAWIQRRYNLPAVNATTQVLPVTGSREALFAFAQTVVDASQPGAL 119

Query: 120 VVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPA 179
           V+CPNPFYQIYEGAALLAGATP + N+DPAR+F     R+  E W + QLVFVCSPGNP 
Sbjct: 120 VLCPNPFYQIYEGAALLAGATPVFANSDPARNFAPAFDRIGAETWAKVQLVFVCSPGNPT 179

Query: 180 GNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDR----YT 235
           G V+SLE+WR LF LSDRHGFVIA+ ECYSEIY  E  PPLG+L+AA +LGR      + 
Sbjct: 180 GAVLSLEDWRELFALSDRHGFVIASDECYSEIYFKEGEPPLGALEAAHKLGRAEGAHPFE 239

Query: 236 NLVAFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRM 295
            LV FSSLSKRSNVPG+RSGFVAGDAALL +FLLYRTYHG AM+P V  AS+AAW+    
Sbjct: 240 RLVMFSSLSKRSNVPGLRSGFVAGDAALLKKFLLYRTYHGGAMNPAVQTASVAAWNDEAH 299

Query: 296 CRKT-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAG---TPGSDTAFARELYGRTGVTV 351
            R   A Y  KF  V P+L  VLDV  P A FYLWA    T  SDT FA  L     VTV
Sbjct: 300 VRNNRAAYARKFAEVTPMLAEVLDVALPDAGFYLWADVSRTGLSDTEFAARLLAEQNVTV 359

Query: 352 LPGSLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFART 395
           LPGS LAREA   NPG  R+R+ALVA  ++C++ A RI  F ++
Sbjct: 360 LPGSYLAREADGINPGANRVRMALVATPEECLEGARRIVAFCKS 403


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: 569
Number of extensions: 22
Number of successful extensions: 6
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: 405
Length adjustment: 31
Effective length of query: 366
Effective length of database: 374
Effective search space:   136884
Effective search space used:   136884
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 RR42_RS11930 RR42_RS11930 (succinyldiaminopimelate aminotransferase)
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.30485.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-184  598.4   0.0   3.2e-184  598.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS11930  RR42_RS11930 succinyldiaminopime


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS11930  RR42_RS11930 succinyldiaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.3   0.0  3.2e-184  3.2e-184       1     395 []       1     401 [.       1     401 [. 0.98

  Alignments for each domain:
  == domain 1  score: 598.3 bits;  conditional E-value: 3.2e-184
                                 TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpe 69 
                                               mnp+l+ l+pyPfekl+ ll+dv+p+  l++i++ iGePkh+tP+f++ al + l++l++yPtt+G+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930   1 MNPRLDLLQPYPFEKLRVLLADVKPNGALPAISFGIGEPKHPTPEFIKTALSNALQGLANYPTTAGSDA 69 
                                               9******************************************************************** PP

                                 TIGR03538  70 lreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidrae.kalvvlPnPfyqiyeGaalla 137
                                               lr+++a+W++rr++lpa v++ +qvlPv+G+realfaf+q+v+d ++  alv++PnPfyqiyeGaalla
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930  70 LRQCMAAWIQRRYNLPA-VNATTQVLPVTGSREALFAFAQTVVDASQpGALVLCPNPFYQIYEGAALLA 137
                                               *****************.**************************9997899****************** PP

                                 TIGR03538 138 gaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasde 206
                                               ga+p+f n++++ +f p fd + +e+W++vql+fvcsPgnPtGavlsle++++l++l+d+++f+iasde
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930 138 GATPVFANSDPARNFAPAFDRIGAETWAKVQLVFVCSPGNPTGAVLSLEDWRELFALSDRHGFVIASDE 206
                                               ********************************************************************* PP

                                 TIGR03538 207 cyselyldeaeaPvGlleaaaelGrdd....fkrllvfhslskrsnvPGlrsGfvaGdaellkeflryr 271
                                               cyse+y+ e e+P+G leaa++lGr +    f+rl++f+slskrsnvPGlrsGfvaGda+llk+fl yr
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930 207 CYSEIYFKEGEPPLGALEAAHKLGRAEgahpFERLVMFSSLSKRSNVPGLRSGFVAGDAALLKKFLLYR 275
                                               ***********************996544449************************************* PP

                                 TIGR03538 272 tyhGcampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPdasfylWlkv..pdgdd 338
                                               tyhG am++avq+as+aaW+de+hvr+nra+y++kfa v+ +l++vld+ lPda+fylW+ v  +   d
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930 276 TYHGGAMNPAVQTASVAAWNDEAHVRNNRAAYARKFAEVTPMLAEVLDVALPDAGFYLWADVsrTGLSD 344
                                               ************************************************************99544679* PP

                                 TIGR03538 339 eafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaeleecveaaerikkll 395
                                               ++fa +l +e+nv+vlpG+yl+rea+g nPG++rvr+alva  eec e+a+ri +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11930 345 TEFAARLLAEQNVTVLPGSYLAREADGINPGANRVRMALVATPEECLEGARRIVAFC 401
                                               *****************************************************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (405 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.17
//
[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