GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Marinobacter adhaerens HP15

Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate GFF3766 HP15_3708 4-aminobutyrate aminotransferase

Query= SwissProt::Q88FI7
         (416 letters)



>FitnessBrowser__Marino:GFF3766
          Length = 425

 Score =  348 bits (894), Expect = e-100
 Identities = 180/398 (45%), Positives = 247/398 (62%), Gaps = 4/398 (1%)

Query: 20  HGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLA 79
           H  NAE+WD DGKR IDF GGIGVLN+GH +P VVEA++AQ  +L H      P+  Y+ 
Sbjct: 28  HATNAELWDADGKRMIDFAGGIGVLNIGHRHPKVVEAVKAQLDKLMHTCQTVMPYEGYVK 87

Query: 80  LMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNL 139
           L E+LS  VPV      ML NSGAEA ENA+K+AR ATGK  +I FDGG+HGRT  T+ +
Sbjct: 88  LAEKLSGVVPVRGHAKVMLANSGAEALENAMKIARAATGKTNVICFDGGYHGRTFYTMAM 147

Query: 140 NGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPV 199
           NGK APY+   G +PG VY  PYP    GV+ ++AL+ +      +    + AA + EPV
Sbjct: 148 NGKAAPYQTDFGPMPGTVYRAPYPVPYHGVSEDEALRGLKMAMKADSPAHNTAAIVIEPV 207

Query: 200 QGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAK 259
            GEGGF A   +F + +R+ CDE  IL+I DE+QSGFGRTG+ FA    G+EPDL+ +AK
Sbjct: 208 LGEGGFYAAPTSFLKEIRKICDENDILMIADEVQSGFGRTGKMFAIEHSGVEPDLMTMAK 267

Query: 260 SIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQE 319
           S+A GMP+ A+VG  + M A     LGGTY+G+P +CAAALA      +E++    +   
Sbjct: 268 SMADGMPISAIVGTDKYMDASGPNSLGGTYTGSPTACAAALAVFDVFKEEDILGKSQALG 327

Query: 320 QAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGS--PAPAQLAKVMEAARARGLL 377
           + +  R+ +W+      ++  +  +G M   E   +  S  P P   A V + A+ +GL+
Sbjct: 328 EKLKQRFSQWQEQ--FAHVDNVRNLGPMAAFELVESKESRTPKPELAAAVTKKAKEKGLI 385

Query: 378 LMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
           L+  G   + +R L P+TIE EVLEEGL I+E+ L E+
Sbjct: 386 LLSCGMYGNTLRFLMPVTIEDEVLEEGLAIVEESLKEV 423


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: 518
Number of extensions: 29
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: 425
Length adjustment: 32
Effective length of query: 384
Effective length of database: 393
Effective search space:   150912
Effective search space used:   150912
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.

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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