GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Rhodobacter viridis JA737

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_110806203.1 C8J30_RS11905 aspartate aminotransferase family protein

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



>NCBI__GCF_003217355.1:WP_110806203.1
          Length = 393

 Score =  178 bits (451), Expect = 3e-49
 Identities = 132/409 (32%), Positives = 186/409 (45%), Gaps = 41/409 (10%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73
           P+    G  + +W  DG RY+D   GI V  LGH  P +V  +  QA +L H +     P
Sbjct: 13  PLAFVRGEGSWLWTEDGSRYLDLGAGIAVNALGHAAPELVATLTEQAGKLWHVSNLYRIP 72

Query: 74  HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDG 127
               LA M   + F    +      TNSG EA E A+K+ R      G   +  I+ F G
Sbjct: 73  EQERLADMLVANTFADTVF-----FTNSGTEACELAVKMVRKYFYEKGQPERSDILTFSG 127

Query: 128 GFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELA 187
            FHGR+ A +   G     K     LPG   HLP+   +                +V+ A
Sbjct: 128 AFHGRSSAAIAAAGTEKMVKGFGPLLPG-FKHLPWGDLE----------------AVKAA 170

Query: 188 VEDV-AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246
           V D  AA + EP+QGEGG       F +ALR  CD  G L++ DE+Q G  RTG+ FA  
Sbjct: 171 VTDTTAAILIEPIQGEGGIRPAPEGFLKALREICDATGTLLVFDEVQCGVARTGRLFAHE 230

Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306
             G+ PD++++AK I GG PLGAV+      + +  G  G TY GNP+ CA     +  +
Sbjct: 231 WAGVTPDVMMVAKGIGGGFPLGAVLATANAASGMTAGTHGSTYGGNPLGCAIGAKMIEIV 290

Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366
           T         R+   +  R E   A+        + G G M G+      G         
Sbjct: 291 TAPGFLEEVSRKAGFLRQRLEGLVAAH-PDIFEEVRGQGLMLGLRCKLPPGD-------- 341

Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
           V++AA A+ LL +P+  A +++RLL  LTI  + + E +  LE     L
Sbjct: 342 VVKAAYAQNLLTVPA--ADNVLRLLPALTITEDDMAEAVRRLEAAATAL 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: 387
Number of extensions: 20
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: 393
Length adjustment: 31
Effective length of query: 385
Effective length of database: 362
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 Sep 24 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