GapMind for catabolism of small carbon sources

 

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

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase

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



>NCBI__GCF_021560695.1:WP_027489558.1
          Length = 408

 Score =  213 bits (542), Expect = 8e-60
 Identities = 146/406 (35%), Positives = 213/406 (52%), Gaps = 33/406 (8%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           + L HG+ A VWDT+G+ Y+DF  GI V  LGH +P ++ A+ AQA +L H + N     
Sbjct: 25  LVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKLWHSS-NVFYTE 83

Query: 76  PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-------ATGKRAIIAFDGG 128
           P L L E+L       +     L NSGAEA E A+K+ R        A  +R I+ F+G 
Sbjct: 84  PPLRLAEELVH--ASGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERRVIVTFNGS 141

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188
           FHGRTLAT+    + A Y+Q    LP    +L +  A+          A++  F    A 
Sbjct: 142 FHGRTLATVTATAQ-AKYQQGYEPLPEGFRYLDFNDAE----------ALEATF----AA 186

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
            DVAA + EPVQGEGG L   P F + +R  CD+   L+++DEIQ G GRTG  FA    
Sbjct: 187 GDVAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHD 246

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
            + PD++ LAK++ GG P+GA++   ++   +  G  G T+ GNP++ A A  +LA+++ 
Sbjct: 247 HVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSS 306

Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368
             +    ERQ   + +   R   +        + G G M G   A+A    A A    V+
Sbjct: 307 PAVLMNVERQANDLRAGLAR--INHELQLFAEVRGRGLMIGAVLADAYKGKAGA----VL 360

Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
           + A  RGLLL+ +G    ++R + PLTI  E L +GL  L   L++
Sbjct: 361 DHAATRGLLLLQAGP--DVLRFVPPLTITDEELADGLARLHAALSD 404


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: 419
Number of extensions: 23
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: 408
Length adjustment: 31
Effective length of query: 385
Effective length of database: 377
Effective search space:   145145
Effective search space used:   145145
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 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