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_RS04135 HSERO_RS04135 amidohydrolase

Query= curated2:Q836H7
         (378 letters)



>FitnessBrowser__HerbieS:HSERO_RS04135
          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:

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