GapMind for Amino acid biosynthesis

 

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

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__Pedo557:CA265_RS18530
          Length = 382

 Score =  160 bits (404), Expect = 8e-44
 Identities = 119/403 (29%), Positives = 189/403 (46%), Gaps = 39/403 (9%)

Query: 13  VHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAA 72
           ++ I ++    + VWD + ++Y+D  GG  V+++GH NP  V  +  Q  ++  Y+ N+ 
Sbjct: 9   LNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYS-NSV 67

Query: 73  PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGR 132
                + L E+L + V         L NSGAEA ENALK+A    G++ +IAF G FHGR
Sbjct: 68  KIPLQVQLAEKLGE-VSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHGR 126

Query: 133 TLATLNLNGK---VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189
           T   + +      VAP  Q        V  LP+   +  +  E+  KA            
Sbjct: 127 TSLAVAVTDNPKIVAPVNQTEN-----VIFLPF---NNEIALEETFKAQGN--------- 169

Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249
           +++A I E +QG GG      +F Q +R  CDE   + I D +Q G+GRTG  ++    G
Sbjct: 170 EISAVIIEGIQGVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSG 229

Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDE 309
           +E D+  +AK +  G P+  +    +       G LG T+ GN ++CAAALA L  M  +
Sbjct: 230 VEADVYTMAKGMGNGFPVAGISIASKFKPW--HGELGTTFGGNHLACAAALAVLEVMEKD 287

Query: 310 NLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369
           NL    E     +++  ++++       +  + G G M GIE         PA+LA V +
Sbjct: 288 NLIKNAEEVGNYLIAELKKFE------QVVEVRGRGLMIGIEL--------PAELAHVKK 333

Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
                  +     K  ++IRLL  L +     +E L   E+ +
Sbjct: 334 ELLFTHHIFTGEAKP-NVIRLLPALNLTKAHADEFLAAFEKAV 375


Lambda     K      H
   0.320    0.137    0.402 

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: 371
Number of extensions: 14
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: 416
Length of database: 382
Length adjustment: 31
Effective length of query: 385
Effective length of database: 351
Effective search space:   135135
Effective search space used:   135135
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