Alignments for a candidate for dapC in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Halorhodospira halophila SL1

Align N-succinyldiaminopimelate-aminotransferase (EC 2.6.1.17) (characterized)
to candidate WP_011814258.1 HHAL_RS07430 succinyldiaminopimelate transaminase

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



>NCBI__GCF_000015585.1:WP_011814258.1
          Length = 399

 Score =  337 bits (863), Expect = 5e-97
 Identities = 192/397 (48%), Positives = 240/397 (60%), Gaps = 9/397 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L  L PYPFE++  LL   G+      PI L IGEP+   P  + + +  NL  ++
Sbjct: 1   MNRGLSELQPYPFERMERLLT--GRRAGPAAPIRLGIGEPQDPPPELLTRVLRDNLDQVA 58

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIP--APDPESEVLPVLGSREALFAFAQTVIDPSAGA 118
            YP+T+G  +LR+AI+ WL RRY +P  A +P+  VLPV G+REALFA AQTVI      
Sbjct: 59  RYPATRGLESLREAIAGWLRRRYRLPEAAINPDEHVLPVAGTREALFAIAQTVIGRGR-P 117

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
            V  PNPFYQIYEGAALL+GA P Y+  +P          +    W+R QL+++ SP NP
Sbjct: 118 YVAMPNPFYQIYEGAALLSGARPLYLPIEPGSGLP-DLDAIEPRTWQRVQLLYLNSPANP 176

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G V   + +R + EL DR+GF+IAA ECYSEIY DE  PP G LQ  +  GR  +   +
Sbjct: 177 TGAVADSDYYRRVLELCDRYGFIIAADECYSEIYADEANPPPGLLQVCQAEGRADFHRCL 236

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMRRMCR 297
            F SLSKRSN PG+RSGFVAGD  L+  FL YRTY G A+   V AAS AAW     +  
Sbjct: 237 VFHSLSKRSNAPGLRSGFVAGDPGLIHAFLRYRTYQGCALPLHVQAASAAAWRDEAHVIE 296

Query: 298 KTAQYRAKFEAVLPILQNVLD-VRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSL 356
             A+YR ++E V  IL   LD V  P A+FYLW  TP  D  F R L+    VTVLPGS 
Sbjct: 297 NRARYRERYEEVCTILAEALDEVAPPPATFYLWPRTPIDDQTFTRRLWEEENVTVLPGSF 356

Query: 357 LAREAHNAN-PGQGRIRIALVAPLDQCVQAAERIAHF 392
           L+R   +   PG GRIR+ALV  L  C++AAERI  F
Sbjct: 357 LSRPGGDGTPPGAGRIRMALVPDLATCIEAAERIRRF 393


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: 609
Number of extensions: 39
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: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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_011814258.1 HHAL_RS07430 (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.20499.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-173  562.5   0.0   2.6e-173  562.3   0.0    1.0  1  lcl|NCBI__GCF_000015585.1:WP_011814258.1  HHAL_RS07430 succinyldiaminopime


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015585.1:WP_011814258.1  HHAL_RS07430 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  562.3   0.0  2.6e-173  2.6e-173       1     395 []       1     394 [.       1     394 [. 0.97

  Alignments for each domain:
  == domain 1  score: 562.3 bits;  conditional E-value: 2.6e-173
                                 TIGR03538   1 mnpnlerlkpyPfeklaellkdvtppadleeialsiGePkhatPafvlealvenleelskyPttkGlpe 69 
                                               mn  l++l+pyPfe++++ll++  +     +i+l iGeP+ ++P++++ +l++nl+++++yP+t+Gl++
  lcl|NCBI__GCF_000015585.1:WP_011814258.1   1 MNRGLSELQPYPFERMERLLTGRRAGPA-APIRLGIGEPQDPPPELLTRVLRDNLDQVARYPATRGLES 68 
                                               89********************988877.89************************************** PP

                                 TIGR03538  70 lreaiaeWlerrfelpag.vdperqvlPvnGtrealfafvqavidraekalvvlPnPfyqiyeGaalla 137
                                               lreaia Wl+rr++lp+  ++p+++vlPv Gtrealfa++q+vi r  +++v +PnPfyqiyeGaall+
  lcl|NCBI__GCF_000015585.1:WP_011814258.1  69 LREAIAGWLRRRYRLPEAaINPDEHVLPVAGTREALFAIAQTVIGRG-RPYVAMPNPFYQIYEGAALLS 136
                                               *****************99*************************986.69******************* PP

                                 TIGR03538 138 gaepyflnctaengfkpdfdavpeevWkrvqllfvcsPgnPtGavlsleelkklleladkydfiiasde 206
                                               ga+p +l+ ++ +g  pd+da++  +W+rvqll+++sP nPtGav + + ++++lel d+y+fiia+de
  lcl|NCBI__GCF_000015585.1:WP_011814258.1 137 GARPLYLPIEPGSG-LPDLDAIEPRTWQRVQLLYLNSPANPTGAVADSDYYRRVLELCDRYGFIIAADE 204
                                               *********99885.7***************************************************** PP

                                 TIGR03538 207 cyselyldeaeaPvGlleaaaelGrddfkrllvfhslskrsnvPGlrsGfvaGdaellkeflryrtyhG 275
                                               cyse+y+dea++P Gll+++++ Gr df+r+lvfhslskrsn+PGlrsGfvaGd  l+++flryrty+G
  lcl|NCBI__GCF_000015585.1:WP_011814258.1 205 CYSEIYADEANPPPGLLQVCQAEGRADFHRCLVFHSLSKRSNAPGLRSGFVAGDPGLIHAFLRYRTYQG 273
                                               ********************************************************************* PP

                                 TIGR03538 276 campiavqlasiaaWedekhvrenralyrekfaavleilgavld.lelPdasfylWlkvpdgddeafar 343
                                               ca+p++vq+as aaW de+hv+enra+yre+++ v +il++ ld +  P a+fylW+++ ++dd++f+r
  lcl|NCBI__GCF_000015585.1:WP_011814258.1 274 CALPLHVQAASAAAWRDEAHVIENRARYRERYEEVCTILAEALDeVAPPPATFYLWPRT-PIDDQTFTR 341
                                               *****************************************997478899*********.5******** PP

                                 TIGR03538 344 alyeeenvkvlpGrylsrea.egvnPGegrvrlalvaeleecveaaerikkll 395
                                               +l+eeenv+vlpG++lsr   +g+ PG+gr+r+alv +l++c+eaaeri++++
  lcl|NCBI__GCF_000015585.1:WP_011814258.1 342 RLWEEENVTVLPGSFLSRPGgDGTPPGAGRIRMALVPDLATCIEAAERIRRFV 394
                                               ******************97256789************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (395 nodes)
Target sequences:                          1  (399 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: 7.39
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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