GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Caulobacter crescentus NA1000

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate CCNA_00620 CCNA_00620 acetylornithine aminotransferase/succinyldiaminopimelate aminotransferase

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



>FitnessBrowser__Caulo:CCNA_00620
          Length = 392

 Score =  179 bits (453), Expect = 2e-49
 Identities = 137/410 (33%), Positives = 198/410 (48%), Gaps = 44/410 (10%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           I +  G    ++D DG+ Y+D   G+ V  LGH +P +V+A++ QA  L H A N     
Sbjct: 13  IDIVRGEGCWLYDQDGRDYLDLAAGVAVNTLGHGDPRLVQALKTQADILWH-ASNLYRLP 71

Query: 76  PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR---GATGKRA---IIAFDGGF 129
              AL  +L+     ++       NSGAEA E A+K AR   GA G+     ++ F   F
Sbjct: 72  AQEALATKLTD---ATFADRVFFANSGAEAVEAAIKTARRWQGAKGRPERYRVLTFGNAF 128

Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGV--TCEQALKAMDRLFSVELA 187
           HGRTLAT++   ++   K R G  P       Y + DT      E A +A+         
Sbjct: 129 HGRTLATISATDQM---KVREGFTP------LYDAFDTTPFNDIEGAARAI--------- 170

Query: 188 VEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPR 247
               AA + EP+QGEGG     P F   LR  CD+  +L+I+DE+Q+G GRTG  FA   
Sbjct: 171 TPQTAAILVEPIQGEGGLTPATPGFLAGLRALCDQHDLLLILDEVQTGIGRTGHLFAHEL 230

Query: 248 LGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASL-AQM 306
            G+ PD++ +AK + GG P+GA +  ++  + +  G  G TY GNP++CA A A L A +
Sbjct: 231 YGVRPDIIAVAKGLGGGFPIGACLATEDAASGMTPGSHGSTYGGNPLACAVASAVLDAVL 290

Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366
               L T   R+  A+V           S    R  G G MRG++          A    
Sbjct: 291 APGFLET--VRERAALVDALLERLLRRHSDLFVRAQGHGLMRGLQ--------VRASARD 340

Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTI-EAEVLEEGLDILEQCLAEL 415
           V+   R  G++ + +G    ++RLL PLTI E E+ E    +L    A L
Sbjct: 341 VVAHLRDFGVMTVAAG--ADVVRLLPPLTISELEIAEAEARLLRAAEAWL 388


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: 379
Number of extensions: 14
Number of successful extensions: 5
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: 392
Length adjustment: 31
Effective length of query: 385
Effective length of database: 361
Effective search space:   138985
Effective search space used:   138985
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