GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate HSERO_RS10805 HSERO_RS10805 succinyldiaminopimelate aminotransferase

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



>FitnessBrowser__HerbieS:HSERO_RS10805
          Length = 403

 Score =  484 bits (1246), Expect = e-141
 Identities = 248/400 (62%), Positives = 298/400 (74%), Gaps = 9/400 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           +NP LD L PYPFEKL+ L A    P     PI+L IGEPKH  PA + QA+  NLAGL+
Sbjct: 1   VNPLLDQLQPYPFEKLKKLFAGI-TPDPAYRPISLGIGEPKHPTPAFIQQALIDNLAGLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSA-GAL 119
            YP+T G  ALR AI+ WL +RY IP PDP +E+LPV GSREALF+  QTV+DP+  GAL
Sbjct: 60  SYPATLGSDALRGAIADWLQKRYDIPRPDPATEILPVNGSREALFSLTQTVVDPTRPGAL 119

Query: 120 VVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNPA 179
           V+CPNPFYQIYEG+A LAGA PY+VN+DP R+F     +VP +VW R QL+FVCSPGNP 
Sbjct: 120 VMCPNPFYQIYEGSAYLAGAQPYFVNSDPKRNFAPDFSQVPQDVWERVQLLFVCSPGNPT 179

Query: 180 GNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLVA 239
           G V++LE+W+ LF LSDR+GFVIA+ ECYSEIY +ED PPLG +QAAR LGRD Y  L++
Sbjct: 180 GAVLTLEDWKELFALSDRYGFVIASDECYSEIYFNED-PPLGGMQAARLLGRD-YRRLIS 237

Query: 240 FSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCR-K 298
           FSSLSKRSNVPGMRSGFVAGDAA+L +FLLYRTYHG+AMSPV+ AAS+ AW      +  
Sbjct: 238 FSSLSKRSNVPGMRSGFVAGDAAILKKFLLYRTYHGAAMSPVIQAASVLAWQDETHVQGN 297

Query: 299 TAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPG----SDTAFARELYGRTGVTVLPG 354
            A+Y  KF  V P+LQ VL+V  P A+FYLWA        SDT FA+ LY    VTVLPG
Sbjct: 298 IAKYVTKFSQVTPLLQEVLEVALPDAAFYLWAKVDKLVNISDTEFAQRLYAEYNVTVLPG 357

Query: 355 SLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           S LAREAH  NPG GRIR+ALVA +++C++AA+RI  F R
Sbjct: 358 SYLAREAHGVNPGAGRIRMALVAEVEECLEAAQRIVAFTR 397


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: 601
Number of extensions: 22
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 HSERO_RS10805 HSERO_RS10805 (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.7541.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.6e-187  607.6   0.0   5.2e-187  607.5   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS10805  HSERO_RS10805 succinyldiaminopim


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS10805  HSERO_RS10805 succinyldiaminopimelate aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  607.5   0.0  5.2e-187  5.2e-187       1     394 [.       1     395 [.       1     396 [. 0.98

  Alignments for each domain:
  == domain 1  score: 607.5 bits;  conditional E-value: 5.2e-187
                                  TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlp 68 
                                                +np l++l+pyPfekl++l++++tp   +++i+l iGePkh+tPaf+++al++nl +l++yP+t G++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805   1 VNPLLDQLQPYPFEKLKKLFAGITPDPAYRPISLGIGEPKHPTPAFIQQALIDNLAGLASYPATLGSD 68 
                                                599***************************************************************** PP

                                  TIGR03538  69 elreaiaeWlerrfelpagvdperqvlPvnGtrealfafvqavidrae.kalvvlPnPfyqiyeGaal 135
                                                +lr aia+Wl++r+++p+  dp++++lPvnG+realf+++q+v+d+++  alv++PnPfyqiyeG+a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805  69 ALRGAIADWLQKRYDIPR-PDPATEILPVNGSREALFSLTQTVVDPTRpGALVMCPNPFYQIYEGSAY 135
                                                ******************.9***************************9779999************** PP

                                  TIGR03538 136 lagaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiia 203
                                                laga+pyf+n++++ +f pdf+ vp++vW+rvqllfvcsPgnPtGavl+le++k+l++l+d+y+f+ia
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805 136 LAGAQPYFVNSDPKRNFAPDFSQVPQDVWERVQLLFVCSPGNPTGAVLTLEDWKELFALSDRYGFVIA 203
                                                ******************************************************************** PP

                                  TIGR03538 204 sdecyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryr 271
                                                sdecyse+y++e+ +P+G ++aa  lGr d++rl+ f+slskrsnvPG+rsGfvaGda++lk+fl yr
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805 204 SDECYSEIYFNED-PPLGGMQAARLLGR-DYRRLISFSSLSKRSNVPGMRSGFVAGDAAILKKFLLYR 269
                                                **********665.*************8.9************************************** PP

                                  TIGR03538 272 tyhGcampiavqlasiaaWedekhvrenralyrekfaavleilgavldlelPdasfylWlkv...pdg 336
                                                tyhG+am++ +q+as+ aW+de+hv+ n a+y  kf++v+ +l++vl++ lPda+fylW+kv   +++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805 270 TYHGAAMSPVIQAASVLAWQDETHVQGNIAKYVTKFSQVTPLLQEVLEVALPDAAFYLWAKVdklVNI 337
                                                *************************************************************9777789 PP

                                  TIGR03538 337 ddeafaralyeeenvkvlpGrylsreaegvnPGegrvrlalvaeleecveaaerikkl 394
                                                 d++fa++ly+e nv+vlpG+yl+rea+gvnPG+gr+r+alvae+eec eaa+ri ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS10805 338 SDTEFAQRLYAEYNVTVLPGSYLAREAHGVNPGAGRIRMALVAEVEECLEAAQRIVAF 395
                                                *******************************************************987 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.39
//
[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:

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:

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