GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Rhodanobacter denitrificans FW104-10B01

Align L-lysine-epsilon aminotransferase; L-lysine aminotransferase; EC 2.6.1.36; Lysine 6-aminotransferase (uncharacterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase

Query= curated2:Q05174
         (450 letters)



>NCBI__GCF_021560695.1:WP_027489558.1
          Length = 408

 Score =  128 bits (322), Expect = 3e-34
 Identities = 130/422 (30%), Positives = 183/422 (43%), Gaps = 49/422 (11%)

Query: 33  DLVLDLEASAGPWLVDAVTGTRYLDLFSFFASAPLGINPSCIVDDPAFVGELAAAAVNKP 92
           +LVLD    A  W  +   G  Y+D  +  A   LG        DP  +  LAA A    
Sbjct: 24  ELVLDHGKGARVWDTE---GRDYVDFGAGIAVNALGHQ------DPDLLAALAAQAHKLW 74

Query: 93  SNPDV-YTVPYAKFVTTFARVLGDPLLPHLFFVDGGALAVENALKAAFDWKAQKLGLDDR 151
            + +V YT P  +         G      +F  + GA A E A+K    W A +     R
Sbjct: 75  HSSNVFYTEPPLRLAEELVHASG--FAERVFLCNSGAEANEAAIKLVRKWAAAQ----GR 128

Query: 152 AVNRLQVLHLERSFHGRSGYTMSLTNTDPSKTARYPKFDWPRIPAPALEHPLTTHAEANR 211
           A  R  ++    SFHGR+  T++ T           K+     P P          E  R
Sbjct: 129 APERRVIVTFNGSFHGRTLATVTAT--------AQAKYQQGYEPLP----------EGFR 170

Query: 212 EAERRALEAAEEAFRAADGMIACFLAEPIQGEGGDNHFSAEFLQAMQDLCHRHDALFVLD 271
             +    EA E  F A D  +A  + EP+QGEGG    +  FL+ +++LC +HDAL VLD
Sbjct: 171 YLDFNDAEALEATFAAGD--VAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLD 228

Query: 272 EVQSGCGLTGTAWAYQQLGLRPDLV----AFGKKTQVCGVMGGGRIGEVESNVFAVSSRI 327
           E+Q G G TGT +A+    + PD+V    A G    +  ++ G ++ EV           
Sbjct: 229 EIQCGMGRTGTLFAHVHDHVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQ-----YGAH 283

Query: 328 SSTWGGNLADMVRATRVLETIERTDLLDSVVQRGKYLRDGLEALAERHPGVVTNARGRGL 387
            +T+GGN      A   L  +    +L +V ++   LR GL A       +    RGRGL
Sbjct: 284 GTTFGGNPMAAAVARVALAKLSSPAVLMNVERQANDLRAGL-ARINHELQLFAEVRGRGL 342

Query: 388 MCAVDLPDT--EQRDAVLRRMYTGHQVIALPCGTRGLRFRPPLTVTESELDQGLEALAAS 445
           M    L D    +  AVL    T   ++ L  G   LRF PPLT+T+ EL  GL  L A+
Sbjct: 343 MIGAVLADAYKGKAGAVLDHAAT-RGLLLLQAGPDVLRFVPPLTITDEELADGLARLHAA 401

Query: 446 LA 447
           L+
Sbjct: 402 LS 403


Lambda     K      H
   0.321    0.136    0.411 

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: 403
Number of extensions: 20
Number of successful extensions: 3
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: 450
Length of database: 408
Length adjustment: 32
Effective length of query: 418
Effective length of database: 376
Effective search space:   157168
Effective search space used:   157168
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 Apr 09 2024. 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