GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_174545208.1 HTA01S_RS19080 aspartate aminotransferase family protein

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



>NCBI__GCF_001592305.1:WP_174545208.1
          Length = 456

 Score =  221 bits (564), Expect = 3e-62
 Identities = 139/414 (33%), Positives = 219/414 (52%), Gaps = 18/414 (4%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           P+ +       + D DG  +ID   G+GV ++G C+P VVEAI  Q+  L H     +  
Sbjct: 48  PVVMDRAFGVTIKDPDGNTFIDLSAGVGVSSVGRCHPKVVEAIHQQSGVLMHAMEVNSTK 107

Query: 75  GPYLALMEQLSQFVPVSY--PLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGR 132
              LA   ++S+ +P             SG++A E A+K A+  TG+  IIAF GG+HG 
Sbjct: 108 RTELAA--KISEIMPEGLRGDCITFFAQSGSDALEAAVKFAKRVTGRHQIIAFHGGYHGV 165

Query: 133 TLATLNLNGKVAPYKQRVGELPGPVYHLPYPSA------DTGVTCEQ-ALKAMDRLFSVE 185
             A+  L    A Y++  G   G V H PYP A       T  + EQ A + +D L +  
Sbjct: 166 WNASNALTTGTA-YRKGYGPFMGGVIHAPYPYAYRFPFDTTHKSAEQIAGEYVDYLLNTP 224

Query: 186 L-AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFA 244
             A +DVAA I EPVQGEGG++   P F Q LR+ CD+ G L+I+DE+Q+G GRTG+ +A
Sbjct: 225 YTAADDVAAVIVEPVQGEGGYVPPSPEFLQLLRKACDKSGALLIVDEVQAGAGRTGKMWA 284

Query: 245 FPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLA 304
               G++PD+L   K + G +P+  +V R +L A +P G +  T++ N +S A AL ++ 
Sbjct: 285 VEHSGVKPDMLTFGKGMGGDVPMAGLVMRSDLAAKIPDGSVPNTFAANSLSAAVALTNIG 344

Query: 305 QMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAP--- 361
            + D  L       +  + +  + +     +PY+G + G G M GIE      +  P   
Sbjct: 345 LLQDPELDLLNRAHQLGLEA--QEYIRGFNNPYVGEVRGRGLMIGIELVEDKATKEPLSG 402

Query: 362 AQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            +L K+M    + G+L++P G+  +++R++  LTI  ++L + LD+  + L  L
Sbjct: 403 EKLGKLMGYVLSHGVLMVPCGRYTNVMRVMPSLTIPRKLLFKALDVFGEGLRTL 456


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: 499
Number of extensions: 27
Number of successful extensions: 6
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: 456
Length adjustment: 32
Effective length of query: 384
Effective length of database: 424
Effective search space:   162816
Effective search space used:   162816
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