GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Phaeobacter inhibens BS107

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF2829 PGA1_c28750 aminotransferase class-III

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



>FitnessBrowser__Phaeo:GFF2829
          Length = 440

 Score =  152 bits (385), Expect = 1e-41
 Identities = 132/422 (31%), Positives = 195/422 (46%), Gaps = 43/422 (10%)

Query: 28  DTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLSQF 87
           D +GKRY+D  GG  V  LGH +  V+ A+Q Q  +L           P  AL + L   
Sbjct: 26  DANGKRYLDGSGGAAVSCLGHSDAEVIAAVQEQVGKLAFAHTGFLTSEPAEALADLLISQ 85

Query: 88  VPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTLATLNLNG 141
            P          + G+EA E A+K+AR      G T +R +IA    +HG TL  L   G
Sbjct: 86  APGDLHRV-YFVSGGSEATEAAIKLARQYHLERGDTTRRHVIARRQSYHGNTLGALAAGG 144

Query: 142 KVAPYKQRVGELPGPVYHLP--YPSADTG---VTCEQALKAMDRLFS--VELAVEDVAAF 194
             A  +Q+   L   + H+   Y   D G      +   +  + L +  + L  E V AF
Sbjct: 145 N-AWRRQQFAPLLIDISHIAPCYEYVDRGDGESRYDYGQRVANELEAEILRLGPETVMAF 203

Query: 195 IFEPVQGE-GGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253
           + EPV G   G +     + + +R  CD+ G+L+I+DE+  G GRTG  FA    G+ PD
Sbjct: 204 MAEPVVGATSGAVPAVEGYFKRIREICDQYGVLLILDEVMCGMGRTGHLFACEADGVAPD 263

Query: 254 LLLLAKSI-AGGMPLGAVVGRKELMAALPKGG----LGGTYSGNPISCAAALASLAQMTD 308
           +L +AK + AG  P+GA++  +++  A+  G      G TY G+P++ AA LA +  + D
Sbjct: 264 ILCIAKGLGAGYQPIGAMLCSRQIYDAIEGGSGFFQHGHTYIGHPVATAAGLAVVRALLD 323

Query: 309 ENL----ATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQ- 363
             L    A  GE    A+V+R+      G  P++G L G G  RGIE      S  P   
Sbjct: 324 RGLVQRSAEMGETLHAALVARF------GQHPHVGDLRGRGLFRGIELVADRESKTPFDP 377

Query: 364 ----LAKVMEAARARGLLLMPSGKAR------HIIRLLAPLTIEAEVLEEGLDILEQCLA 413
                 K+ +AA   GL+  P    R      HI+ L  P  +  + + E  D LE  L 
Sbjct: 378 GLGIAGKLKKAAFEAGLICYPMAGTRDGRNGDHIL-LAPPFILSEDQIGEITDKLEVALD 436

Query: 414 EL 415
           ++
Sbjct: 437 QV 438


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: 475
Number of extensions: 24
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: 416
Length of database: 440
Length adjustment: 32
Effective length of query: 384
Effective length of database: 408
Effective search space:   156672
Effective search space used:   156672
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: 51 (24.3 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:

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