GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Marinobacter adhaerens HP15

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate GFF1057 HP15_1036 transcriptional regulator, GntR family with aminotransferase domain protein

Query= reanno::acidovorax_3H11:Ac3H11_1358
         (401 letters)



>FitnessBrowser__Marino:GFF1057
          Length = 480

 Score =  144 bits (363), Expect = 5e-39
 Identities = 118/387 (30%), Positives = 179/387 (46%), Gaps = 14/387 (3%)

Query: 14  LARRAERMNPSVIREI---LKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPA 70
           + R   R  P   RE+   L   E+  ++ LA  +P P   P+      S    A  G  
Sbjct: 88  MRRHRSRPVPVSAREMALDLCADEQKRMVPLATAIPHPDYLPLRQIQH-STLWAARRGLE 146

Query: 71  ALQYAASEGYAPLRQAIAD---FLPWDVDADQILITTGSQQALDLIAKVLIDENSRVLVE 127
            L YA   G    R+ IA     L   V  D +L T G+Q+A+ L  + +      V VE
Sbjct: 147 TLDYAFP-GKESFRRQIAQRMATLGVPVTPDDVLATNGAQEAIILALRAVTQPGDIVAVE 205

Query: 128 TPTYLGALQAFTPMEPSVVAVASD-DEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGR 186
           +P++ G LQA   +   V+ + +   EG+ ++ L+  +     KA    V+ N  NP G 
Sbjct: 206 SPSFPGILQALEVVGLKVIEIPTHPSEGLSLEGLQLALEQWPLKA--CVVVTNHSNPMGA 263

Query: 187 TMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARN-PEGCIYMGSFSKVLA 245
            M++ R+  LV   A   +PL+ED+ YGDL      P P  A +  +  IY  SFSK ++
Sbjct: 264 QMSDERKKQLVSMLAAAAVPLIEDDIYGDLHHTGDRPKPAKAFDRADNVIYCSSFSKTIS 323

Query: 246 PGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQ 305
           PGLRLG++V P        Q K   +L T    Q  VA  ++    DR++ + R  Y++ 
Sbjct: 324 PGLRLGWMV-PGRHMASARQHKYFVNLATSSIPQMAVAHFLEQGGYDRYLRSARQHYREA 382

Query: 306 CEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYA 365
            E M  A+ +     G   +RP GG  LWV+LP+G+S  E+  +A   ++   PG  F  
Sbjct: 383 TERMRTAVARAFPE-GTAVSRPQGGFVLWVQLPDGVSGTEVYHRARAEDINVAPGLMFST 441

Query: 366 DNADPRTLRLSFVTSTVEQIATGIAAL 392
            +     LRL+      E+I   +A L
Sbjct: 442 ADKYDNCLRLNSANPWSERIEHAVARL 468


Lambda     K      H
   0.318    0.134    0.392 

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: 454
Number of extensions: 24
Number of successful extensions: 5
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: 401
Length of database: 480
Length adjustment: 32
Effective length of query: 369
Effective length of database: 448
Effective search space:   165312
Effective search space used:   165312
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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