GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapX in Marinobacter adhaerens HP15

Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF835 HP15_814 aspartate aminotransferase

Query= SwissProt::P16524
         (393 letters)



>FitnessBrowser__Marino:GFF835
          Length = 416

 Score =  178 bits (452), Expect = 2e-49
 Identities = 116/383 (30%), Positives = 200/383 (52%), Gaps = 7/383 (1%)

Query: 6   NPKAREIEISGIRKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNA 65
           NP  + I + GIR+  N+ A  +DVI L+IGQPD  TP HV  A   A++   T YT +A
Sbjct: 35  NPAMQAIPVPGIRRMVNMAATMKDVIHLSIGQPDLPTPKHVIDAYIDALNAGQTGYTMDA 94

Query: 66  GYLELRQAVQLYMKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPG 125
           G  EL  A++ Y  K+ +     ++ I+IT+GA++A+  A     +PG + I+  P +  
Sbjct: 95  GLPELLVALRDYYGKRYNRKLTRDN-ILITSGATEAMYLAISATSAPGRQFIVTDPSFLL 153

Query: 126 YEPIINLCGAKPVIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELK 184
           Y P+I + G +   V T   +  +L    +  A+ P T  ++L  P+NPTG       ++
Sbjct: 154 YAPLIRMNGGEVKFVQTRAENNHQLDPDEVIKAMGPRTYALILNNPNNPTGAVYPRSTVE 213

Query: 185 SIAALLKGRNVFVLSDEIYSELTYDRPHYSIATYLR---DQTIVINGLSKSHSMTGWRIG 241
           +I      R + V +DE+Y  L +D   ++         D  + I+  SK++SM G R+G
Sbjct: 214 TILEECAYRGIQVYADEVYDHLIFDDEDFASVLNCSMDLDNIMCISSFSKTYSMAGLRVG 273

Query: 242 FLFAPKDIAKHILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL 301
           ++ A +   K + + H +  S A++ SQ A + A+T        M + Y++R D V + +
Sbjct: 274 WVIASQAAIKSLRRFHMFTTSVANTPSQFAGVAALTGDQQCVRDMVDIYRERRDKVVELV 333

Query: 302 -VSMGLDVVKPSGAFYIFPSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360
             +  +   KP GAF+ FP +    +   D ++ +L++ GV +VPG +F       VR+S
Sbjct: 334 DQTPYMTGYKPGGAFFAFPDLPPH-VDGSDLALRMLKETGVCMVPGDAFGEGCTNAVRIS 392

Query: 361 FACSMDTLREGLDRLELFVLKKR 383
           F+ + + L E  DR+  ++ K++
Sbjct: 393 FSTTCEKLEEAFDRVIPWMAKQQ 415


Lambda     K      H
   0.319    0.135    0.388 

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: 349
Number of extensions: 18
Number of successful extensions: 6
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: 393
Length of database: 416
Length adjustment: 31
Effective length of query: 362
Effective length of database: 385
Effective search space:   139370
Effective search space used:   139370
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