GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Klebsiella michiganensis M5al

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= SwissProt::Q88FI7
         (416 letters)



>FitnessBrowser__Koxy:BWI76_RS26375
          Length = 421

 Score =  335 bits (858), Expect = 2e-96
 Identities = 173/411 (42%), Positives = 243/411 (59%), Gaps = 3/411 (0%)

Query: 3   QESISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQAT 62
           Q++  + + ++    +    NA +WD +G   IDF  GI VLN GH +P ++ A++ Q  
Sbjct: 11  QQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQ 70

Query: 63  RLTHYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAI 122
             TH A+   P+  Y+ L E+++   P+  P       +GAEA ENA+K+AR  TG+  +
Sbjct: 71  AFTHTAYQIVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPGL 130

Query: 123 IAFDGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLF 182
           I F GGFHGRT  T+ L GKVAPYK   G  PG VYH  YP+A  G+T   A+K++DR+F
Sbjct: 131 ITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIF 190

Query: 183 SVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQR 242
             ++A + VAA + EP+QGEGGF    P F QALR  CD  GIL+I DE+Q+GF RTG+ 
Sbjct: 191 KADIAADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKL 250

Query: 243 FAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS 302
           FA     ++PDL+ +AKS+AGG PL  VVGR E+M A   GGLGGTY+GNP++ AAA A 
Sbjct: 251 FAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGNPLAVAAAHAV 310

Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANAD-GSPAP 361
           L  + +E L    ER    +     + + S   P I  + G G+M  +EF +   G P+ 
Sbjct: 311 LDVIEEEQLCQRAERLGSHLKEVLNQARQS--CPAIADVRGQGSMVAVEFNDPQTGEPSA 368

Query: 362 AQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412
               ++ + A+  GLLL+  G   ++IR L PLTI      + LDIL + L
Sbjct: 369 EITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419


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: 516
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: 416
Length of database: 421
Length adjustment: 32
Effective length of query: 384
Effective length of database: 389
Effective search space:   149376
Effective search space used:   149376
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 Apr 09 2024.

Links

Downloads

Related tools

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