GapMind for catabolism of small carbon sources

 

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

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

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



>lcl|FitnessBrowser__Pedo557:CA265_RS18530 CA265_RS18530 aspartate
           aminotransferase family protein
          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 Sep 17 2021. The underlying query database was built on Sep 17 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.

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