GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapL in Pedobacter sp. GW460-11-11-14-LB5

Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate CA265_RS17965 CA265_RS17965 N-acyl-L-amino acid amidohydrolase

Query= SwissProt::D5E0A1
         (375 letters)



>FitnessBrowser__Pedo557:CA265_RS17965
          Length = 434

 Score =  206 bits (524), Expect = 1e-57
 Identities = 130/358 (36%), Positives = 193/358 (53%), Gaps = 24/358 (6%)

Query: 3   ENEFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTW--KTGLFVKVHGTNP 60
           E + +  RR+ H+ PELG  EV+T   +  ++ +L    ++VKT   KTG+   + G  P
Sbjct: 35  EQKVIAWRRDFHEHPELGNTEVRTAGIIAKHLESLG---IQVKTGVAKTGVVGVLKGGKP 91

Query: 61  TKTIGYRADIDGLPITEETNYSFQS--------QHEGLMHACGHDMHMAIGLGVLTYFA- 111
              +  RAD+DGLP+TE  +  F S        Q  G+MHACGHD H+AI +GV    A 
Sbjct: 92  GPVVALRADMDGLPVTERVDVPFASKVKTQYNGQEVGVMHACGHDSHVAILMGVAEVLAS 151

Query: 112 -QHEIKDNVLFIFQPAEEG-----PGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIA 165
            Q +I+  V FIFQPAEEG      GGA  M++  +++    D IF LH+  +  VG + 
Sbjct: 152 MQKDIQGTVKFIFQPAEEGVPAGDEGGAALMIKEGVLENPKVDVIFGLHINSQTEVGDVT 211

Query: 166 LKEGLLFANTSELFIDLKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDS-AV 224
            + G   A  +++ I + G+  H AYP  + D VV + Q+++ LQTIV+RN++  ++  V
Sbjct: 212 YRPGGTMAAVNDMKITVTGRQAHGAYPWNSIDPVVVSAQIINSLQTIVSRNLNVTENPGV 271

Query: 225 ITVGKIQGGTVQNIIAERARIEGTIRTLSPESMTRVKERIEAIV-KGVEV-GYQCETAID 282
           +T+G I GG   NII E+  + GT+R  S E      ERI+ IV K  E  G   E  I 
Sbjct: 272 VTIGAINGGVRSNIIPEKVEMLGTVRNFSKEDEAMFIERIKTIVTKTAEAGGATAEVKIP 331

Query: 283 YGCMYHQVYNHHEVTREFMEFAKEQTDVDVIECKEAMTG-EDFGYMLKDIPGFMFWLG 339
           Y   Y   +NH  +T + +   +     D ++ K  +TG EDF +  + IPG   +LG
Sbjct: 332 YSNHYPVTFNHIALTEKMLPSMQNTAGKDHVKLKPPVTGAEDFSFFQEKIPGLFVFLG 389


Lambda     K      H
   0.320    0.137    0.410 

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: 442
Number of extensions: 22
Number of successful extensions: 8
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: 375
Length of database: 434
Length adjustment: 31
Effective length of query: 344
Effective length of database: 403
Effective search space:   138632
Effective search space used:   138632
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