GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Amantichitinum ursilacus IGB-41

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_053937056.1 WG78_RS06780 aspartate aminotransferase family protein

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



>NCBI__GCF_001294205.1:WP_053937056.1
          Length = 400

 Score =  193 bits (491), Expect = 7e-54
 Identities = 134/409 (32%), Positives = 204/409 (49%), Gaps = 50/409 (12%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80
           G  + VWD  GK YIDF GGI V +LGHC+P +V A+  Q  +L H + N   + P LAL
Sbjct: 26  GAGSRVWDQAGKEYIDFGGGIAVNSLGHCHPELVAALTEQGNKLWHIS-NVFTNEPALAL 84

Query: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGAT------GKRAIIAFDGGFHGRTL 134
            + L   V  ++       NSGAEA E ALK+AR A+       K  +++    FHGRT 
Sbjct: 85  AKTL---VEHTFAERVFFCNSGAEANEAALKLARRASIEKYGERKNKVLSALNSFHGRTF 141

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVED-VAA 193
            T+++ G+   Y    G  P  + H  Y                + L S+E  ++D  A 
Sbjct: 142 FTVSVGGQ-PKYSDGFGPKPAGIEHFKY----------------NDLASLEALIDDDTAC 184

Query: 194 FIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPD 253
            I EP+QGEGG       F Q +R  CD+   L+I DE+QSG GRTG  +A+   G+ PD
Sbjct: 185 VIIEPIQGEGGVTPATQEFLQGVRALCDKFNALLIFDEVQSGNGRTGSLYAYMDFGVVPD 244

Query: 254 LLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMT-DENLA 312
           +L  AK + GG P+GA++  +++   L  G  G TY GNP++ A A  +++ +T  E L+
Sbjct: 245 ILSTAKGLGGGFPIGAMLTTEKVAKHLVAGTHGTTYGGNPLATAVAGTAISIITRPETLS 304

Query: 313 TWGERQE------QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAK 366
               + E      QAI  +Y         P +  + G+G + G++      +    +   
Sbjct: 305 GVKAKSERIRAGLQAIADKY---------PVVAEIRGMGLLIGVQLK----AEYAGRSRD 351

Query: 367 VMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
           V+ AA   G+L++ +G    ++R    L I  + ++ GL  +E+  A L
Sbjct: 352 VLNAAAEEGVLVLAAGP--DVVRFAPSLVISDDEIDAGLARVEKAFARL 398


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: 420
Number of extensions: 17
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: 400
Length adjustment: 31
Effective length of query: 385
Effective length of database: 369
Effective search space:   142065
Effective search space used:   142065
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