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_027490801.1 LRK54_RS04500 acetyl ornithine aminotransferase family protein

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



>NCBI__GCF_021560695.1:WP_027490801.1
          Length = 444

 Score =  260 bits (665), Expect = 5e-74
 Identities = 158/421 (37%), Positives = 224/421 (53%), Gaps = 23/421 (5%)

Query: 4   ESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATR 63
           E IS S    +P  +SHGR  EVWD DG R++DF+ GI V   GH +P VV+A+Q  A +
Sbjct: 28  EVISPSYPRDYPFVMSHGRGTEVWDVDGNRFLDFMAGIAVCATGHAHPQVVKAVQDAAAK 87

Query: 64  LTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAII 123
             H + +   H     L E+L+   P+  P    +  SG EA E ALK+AR  TG+   I
Sbjct: 88  FLHISSDYW-HEEMTGLGERLAAVAPLGAPAMSFICQSGTEAVEGALKLARYVTGRPRFI 146

Query: 124 AFDGGFHGRTLATLNLNGKVAPYKQRVGELP--GPVYHLPYPSADTGVTC--EQALKAMD 179
            F GGFHGRT  +L+     + Y Q+ G  P    V H+PYP+    +    +Q    +D
Sbjct: 147 GFLGGFHGRTFGSLSFTS--SKYTQQKGFSPTLAGVTHVPYPNPYRPLFAGDDQGAAVLD 204

Query: 180 ---RLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGF 236
               LF   +   +VAA + EP+QGEGG+L     F   LR  CDE GIL+I DE+QSG 
Sbjct: 205 YIRMLFQRSVPPSEVAAILIEPMQGEGGYLTPPDGFLAGLRALCDEHGILLIFDEVQSGI 264

Query: 237 GRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISC 296
           GRTG+ FA    G++PD++  AK +  G+P+GAV+ +K +M+   +G  G TY GNP++C
Sbjct: 265 GRTGRMFACEHWGVQPDIITSAKGLGSGLPIGAVIAKKSIMSQWKRGAHGNTYGGNPVTC 324

Query: 297 AAALASLAQMTDENLATWGERQEQAIVSRYERWKASGLS---PYIGRLTGVGAMRGIEFA 353
           AAA A+L      +L   G     A V  +   +   L    P IG + G G   G+E  
Sbjct: 325 AAANATL------DLVRGGLMDNAARVGDHFMARLRELQRDYPCIGEVRGKGLWIGMELI 378

Query: 354 NADG--SPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQC 411
             DG  +PA A    V++ A   GLLL+  G +   +R + PL +    ++E + +L   
Sbjct: 379 EDDGKKTPATALCEAVVQRAFHNGLLLLSCGTS--TVRFMPPLNVSVGEVDEAIALLRSS 436

Query: 412 L 412
           L
Sbjct: 437 L 437


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: 551
Number of extensions: 34
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: 444
Length adjustment: 32
Effective length of query: 384
Effective length of database: 412
Effective search space:   158208
Effective search space used:   158208
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