GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Klebsiella michiganensis M5al

Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate BWI76_RS20205 BWI76_RS20205 aminotransferase AlaT

Query= curated2:O67781
         (394 letters)



>FitnessBrowser__Koxy:BWI76_RS20205
          Length = 405

 Score =  153 bits (386), Expect = 1e-41
 Identities = 111/360 (30%), Positives = 183/360 (50%), Gaps = 21/360 (5%)

Query: 20  ITAKAKELRAKGVDVIGFGAGEP---DFDTPDFIKEACIRALREGKTKYAPSAGIPELRE 76
           +  +AK L  +G  V+    G P    FD PD I    IR L   +  Y+ S G+   R+
Sbjct: 21  VLKEAKRLEEEGNKVLKLNIGNPAPFGFDAPDEILVDVIRNLPTSQG-YSDSKGLYSARK 79

Query: 77  AIAEKLLKENKVEYKPSEIVVSAGAKMVLFLIFMAILDEGDEVLLPSPYWVTYPEQIRFF 136
           AI +        +    +I +  G   ++     A+L+ GDE+L+P+P +  +   +   
Sbjct: 80  AIMQHYQARGMRDVTVEDIYIGNGVSELIVQAMQALLNSGDEMLVPAPDYPLWTAAVSLS 139

Query: 137 GGVPVEVPLKKEKGFQLSLEDVKEKVTERTKAIVINSPNNPTGAVYEEEELKKIAEFCVE 196
            G  V     +   +   L+D++ K+T RT+ IVI +PNNPTGAVY +E L +I E   +
Sbjct: 140 SGKAVHYLCDESSDWFPDLDDIRAKITPRTRGIVIINPNNPTGAVYSKELLMEIVEIARQ 199

Query: 197 RGIFIISDECYEYFVYGDAKFVSPASFSDEVKNITFTVNAFSKSYSMTGWRIGYVAC--P 254
             + I +DE Y+  +Y +A+  S A  + ++  ITF  N  SK+Y + G+R G++    P
Sbjct: 200 HNLIIFADEIYDKILYDEAQHHSIAPLAPDLLTITF--NGLSKTYRVAGFRQGWMVLNGP 257

Query: 255 EEYAK-------VIASLNSQSVSNVTTFAQYGALEALKNPKS-KDFVNEMRNAFERRRDT 306
           +++AK       ++AS+  +  +NV   AQ+    AL   +S  +F+      +E +R+ 
Sbjct: 258 KKHAKGYIEGLEMLASM--RLCANVP--AQHAIQTALGGYQSISEFIVPGGRLYE-QRNR 312

Query: 307 AVEELSKIPGMDVVKPEGAFYIFPDFSAYAEKLGGDVKLSEFLLEKAKVAVVPGSAFGAP 366
           A E ++ IPG+   KP+GA Y+FP   A    +  D K+    L + KV +V G+AF  P
Sbjct: 313 AWELINDIPGVSCTKPKGALYMFPKIDAKRFNIHDDQKMVLDFLLQEKVLLVQGTAFNWP 372


Lambda     K      H
   0.317    0.135    0.383 

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: 392
Number of extensions: 23
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: 394
Length of database: 405
Length adjustment: 31
Effective length of query: 363
Effective length of database: 374
Effective search space:   135762
Effective search space used:   135762
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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