Alignments for a candidate for dapC in Herbaspirillum seropedicae SmR1

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.19371.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.02
//
[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