GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Brucella inopinata BO1

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

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



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  181 bits (459), Expect = 4e-50
 Identities = 136/424 (32%), Positives = 206/424 (48%), Gaps = 56/424 (13%)

Query: 13  VHPITLSHGRNA-------EVW--DTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63
           VHP+  ++ R A        +W    DG+RYIDF  GI V +LGH +P +VE ++ QA +
Sbjct: 7   VHPLYDTYNRAALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQAEK 66

Query: 64  LTHYAFNAAPHGPYLALMEQLSQ-FVPVSYPLAGMLTNSGAEAAENALKVAR------GA 116
           L H +     +   +   E+L +  V  ++      TNSGAEA E A+K AR      G 
Sbjct: 67  LWHLS-----NIYEIPAQEKLGRRLVENTFADKVFFTNSGAEALECAIKTARRYQYVSGH 121

Query: 117 TGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALK 176
             +  II F+G FHGRTLAT+   G+ A Y +  G        +P+         E AL+
Sbjct: 122 PERFRIITFEGAFHGRTLATIAAGGQ-AKYLEGFGPKVEGFDQVPFGD-------EAALR 173

Query: 177 AMDRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGF 236
           A            + A  + EP+QGEGG  A    F + +R+ CDE G+L+++DE+Q+G 
Sbjct: 174 AA--------ITPETAGILLEPIQGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGV 225

Query: 237 GRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISC 296
           GRTG+ FA    GI PD++ +AK I GG P+GA +   E    +  G  G TY GNP+  
Sbjct: 226 GRTGKFFAHEWAGIRPDIMAIAKGIGGGFPIGACLATAEAAKGMTAGMHGTTYGGNPLGM 285

Query: 297 AAALA----SLAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEF 352
           A   A     LA    EN+       +Q + S  +R+        +  + G G + G++ 
Sbjct: 286 AVGNAVLDVVLADGFMENVQATALVMKQGLASLVDRY-----PNVVSEIRGRGLLMGLKC 340

Query: 353 ANADGSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
              + S        +++A R   +L + +G   +++RLL PL    E   E L  +E  +
Sbjct: 341 VVPNTS--------LIQALRDEHVLSVGAGD--NVVRLLPPLITTPEEAREALKHIETAV 390

Query: 413 AELN 416
             L+
Sbjct: 391 ERLS 394


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: 430
Number of extensions: 22
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: 403
Length adjustment: 31
Effective length of query: 385
Effective length of database: 372
Effective search space:   143220
Effective search space used:   143220
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