GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Herbaspirillum seropedicae SmR1

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate HSERO_RS05715 HSERO_RS05715 amidohydrolase

Query= curated2:B1YJ90
         (370 letters)



>FitnessBrowser__HerbieS:HSERO_RS05715
          Length = 403

 Score =  207 bits (526), Expect = 5e-58
 Identities = 129/372 (34%), Positives = 194/372 (52%), Gaps = 13/372 (3%)

Query: 7   MRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYRA 66
           +RR+LH  PE  F+E +T   ++ +++S     V+     TGV   + G    R I  RA
Sbjct: 21  LRRDLHAHPELRFEEHRTADVVVRELQSLGYT-VTRGLGGTGVVASLAGADPQRGIVLRA 79

Query: 67  DIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVV-FLFQPAE 125
           D+D LPI EA      S   G MHACGHD H  + LG  R + + P++   V F+FQP E
Sbjct: 80  DLDALPIVEANDFAHASCTHGVMHACGHDGHTVMLLGAARLLKQGPMLPGSVHFVFQPGE 139

Query: 126 EGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQSG 185
           EG  GA  MI   LFE++    ++G+H  P  P G    RPG + A+   + ITI G+  
Sbjct: 140 EGGAGARKMIDDGLFEQFPTEAVFGMHNWPGLPAGQFGLRPGPIMAAGSRLKITITGKGA 199

Query: 186 HAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLDG 245
           HAA PHL +D +    ++++Q QTI +R  +P++ +VI++    AG  +NVI  RA L G
Sbjct: 200 HAAQPHLGLDPIPLACSMVLQCQTIAARHKDPVDPAVISVCMFHAGDTDNVIPDRAELRG 259

Query: 246 TMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVKMN 305
           T+R L+ T  +KL++ +R +   +  ++G K++++F   Y   +N     D     ++  
Sbjct: 260 TIRTLSSTLQQKLQEDIRRMCHALAEAYGAKVEVEFFQYYPATINTPAETDFCERVIRQT 319

Query: 306 AN----YIECDAAMTGEDFGFMLKEIPGMMFWLG---VNNATSGLHQP--TLNPD--EEA 354
                      A MT EDFGFML+E PG    +G    + A+  LH P    N D  E  
Sbjct: 320 FGDDRIRTGIPANMTSEDFGFMLEERPGAYVLIGNAPQDRASHSLHHPHYDFNDDIIEAG 379

Query: 355 IPFVINLLDHYF 366
           + + + L   YF
Sbjct: 380 VRYWVALAQGYF 391


Lambda     K      H
   0.323    0.140    0.417 

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: 465
Number of extensions: 31
Number of successful extensions: 4
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: 370
Length of database: 403
Length adjustment: 30
Effective length of query: 340
Effective length of database: 373
Effective search space:   126820
Effective search space used:   126820
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)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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