GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapL in Herbaspirillum seropedicae SmR1

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate HSERO_RS04135 HSERO_RS04135 amidohydrolase

Query= curated2:Q836H7
         (378 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS04135 HSERO_RS04135
           amidohydrolase
          Length = 402

 Score =  208 bits (529), Expect = 2e-58
 Identities = 139/381 (36%), Positives = 199/381 (52%), Gaps = 25/381 (6%)

Query: 5   EQEELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQV--RTWQTGILVFIEGKN 62
           ++ +L++IRR LH  PE+  EEK T +F+    D ++   L V       G++  +    
Sbjct: 13  KEMDLVSIRRHLHAHPELRFEEKRTASFVA---DMLRSYGLTVAENIGGYGVVATLRKGK 69

Query: 63  PQKTIGWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQ-QPDNN 121
             + I  RAD+D LP+ E+   +  S   G MHACGHD H T+ LG  + LS++ + D  
Sbjct: 70  STRAIALRADMDALPMSEQNDFSHISTCAGKMHACGHDGHTTMLLGAARRLSREVEFDGT 129

Query: 122 FLFLFQPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEV 181
             F+FQPAEE  AG  LM ED  F  +  D  + +H  P LP G+   R G L A++   
Sbjct: 130 VHFVFQPAEEGGAGARLMIEDGLFERFPADAIFGVHNWPGLPAGSFGLRPGPLMASSNTF 189

Query: 182 NITLKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGTACNV 241
           + TL G+G H A PH++ D VLAA  L    Q+IV+RN++P   AV++    H GTA NV
Sbjct: 190 SATLFGRGAHGAQPHRSIDPVLAAAQLTLAWQSIVTRNINPNHRAVISVTQLHTGTADNV 249

Query: 242 IAEEATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVNEPACT 301
           I E+ATLSGT+R+  AET +  + R+  I+E I Q F   V  H ++  Y  VVN P  T
Sbjct: 250 IPEQATLSGTVRSFDAETLDLIEHRMAAIAEAIGQMFDLRVQFHFERL-YPAVVNHPEAT 308

Query: 302 TNFIEYMSKQATVQFQQ----APVAMTGEDFGYLLSKVPGTMFWLG------------VA 345
              ++ M   A V  +Q       A   EDF + L   PG   +LG             A
Sbjct: 309 QQAMQAM--MAAVGAEQVDGDTEPAFASEDFAFYLQHKPGCYAFLGNGVIADGKQAGSQA 366

Query: 346 SPYSLHSAKFEPNEEALLFGV 366
           +   LHS  ++ N++ +  GV
Sbjct: 367 TSRELHSPFYDFNDDIIDAGV 387


Lambda     K      H
   0.319    0.135    0.398 

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: 368
Number of extensions: 16
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: 378
Length of database: 402
Length adjustment: 30
Effective length of query: 348
Effective length of database: 372
Effective search space:   129456
Effective search space used:   129456
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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