GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase

Query= SwissProt::Q88FI7
         (416 letters)



>FitnessBrowser__Cola:Echvi_3848
          Length = 381

 Score =  184 bits (468), Expect = 3e-51
 Identities = 139/402 (34%), Positives = 202/402 (50%), Gaps = 43/402 (10%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           +T      + +WD  G  Y+D  GG  V+++GH +P   + I+ Q   +  Y+ N+    
Sbjct: 12  VTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYS-NSVQIP 70

Query: 76  PYLALMEQLSQFVPVSYPLAGM-LTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTL 134
               L  +L Q     YP   + L NSGAEA ENALK+A   TGK+  IAF  GFHGRT 
Sbjct: 71  IQKELATKLGQLS--GYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHGRTS 128

Query: 135 ATLNLNGK---VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDV 191
             + L      +AP+    G     V+ LP+            L+A+++    +LA   +
Sbjct: 129 GAVALTDNPKIIAPFNAHEG-----VHILPFND----------LEAVEK----QLATGTI 169

Query: 192 AAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL-GI 250
           A  I E +QG GG    DPAF   L     + G  +I+DE+QSG+ R+G+ FA   + G+
Sbjct: 170 AGVIVEGIQGVGGIQVPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGL 229

Query: 251 EPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDEN 310
           +PDL+ +AK +  G P+G V+   E  A+   G LG T+ GN ++CAAALA L  + +EN
Sbjct: 230 KPDLITVAKGMGNGFPIGGVLISPEFKAS--HGLLGTTFGGNHLACAAALAVLEVIDEEN 287

Query: 311 LATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEA 370
           L T      +AI++  E  K +G++     + G G M G + A   G   P + A + E 
Sbjct: 288 LITAAAENGKAIMAALE--KVAGVT----EVRGKGLMIGFDLATEAG---PVRAALIHEH 338

Query: 371 ARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
               G     S   +H IRLL PL IE + L   L+ LE  L
Sbjct: 339 KIFTG-----SAGGKHTIRLLPPLNIEPKALTLFLEKLETVL 375


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: 398
Number of extensions: 23
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: 381
Length adjustment: 31
Effective length of query: 385
Effective length of database: 350
Effective search space:   134750
Effective search space used:   134750
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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