GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Paraburkholderia bryophila 376MFSha3.1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate H281DRAFT_03179 H281DRAFT_03179 4-aminobutyrate aminotransferase apoenzyme

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_03179
          Length = 429

 Score =  218 bits (555), Expect = 3e-61
 Identities = 140/390 (35%), Positives = 205/390 (52%), Gaps = 37/390 (9%)

Query: 23  FIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGNGYTNEP 82
           F   R + + LWD +G+ +IDFA GIAV   GH HP++  A+ +Q  +F HT   Y   P
Sbjct: 26  FYAERAQNAELWDVEGRRFIDFAAGIAVCNTGHRHPKIVAAIRDQLDRFTHTA--YQIVP 83

Query: 83  V---LRLAKKLIDATFAD---RVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKN 136
               + LA+KL +    D   +  F  +GAEA E A+K+AR        + + G++AF  
Sbjct: 84  YASYVELAEKLNERAPGDHPKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFTG 137

Query: 137 AFHGRTLFTVSAGGQPA-YSQDFAPLPADIRHAAY----NDINSASAL----------ID 181
            FHGRTL  ++  G+ A Y   F P P+D+ HA +    + +++A +L          ID
Sbjct: 138 GFHGRTLMGMALTGKVAPYKAGFGPFPSDVFHAPFPNPLHGVSTADSLKAIEFLFKADID 197

Query: 182 DS-TCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMH 240
                A+I EP+QGEGG  PA   F++ LR+LCN H  LLI DEVQTG  RTG+L+A  H
Sbjct: 198 PKRVAAIIFEPVQGEGGFYPAPAEFVRALRKLCNEHGILLIADEVQTGFARTGKLFAMHH 257

Query: 241 YGVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELIN 300
           Y V PDL+T AK+L GG P+  ++   +       G  G TY GNPLA A A  VL++I+
Sbjct: 258 YDVVPDLMTVAKSLAGGMPLSGVIGRADVMDAAAPGGLGGTYAGNPLAVAAALAVLDIID 317

Query: 301 TPEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL-----NADYAGQAKQIS 355
             ++        D    +L  + +     ++VRG G ++             A   K++ 
Sbjct: 318 EEKLCERATILGDRVKAKLIALQNEAPQIADVRGPGGMVAVEFCKPGSTEPDAEFTKRVQ 377

Query: 356 QEAAKAGVMVLIAG--GNVVRFAPALNVSE 383
             A K G+++L+ G   NVVRF   L + +
Sbjct: 378 TRALKRGLLLLVCGVYSNVVRFLFPLTIED 407


Lambda     K      H
   0.319    0.135    0.406 

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: 446
Number of extensions: 26
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: 406
Length of database: 429
Length adjustment: 32
Effective length of query: 374
Effective length of database: 397
Effective search space:   148478
Effective search space used:   148478
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 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