GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Shewanella amazonensis SB2B

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938533 Sama_2636 4-aminobutyrate aminotransferase (RefSeq)

Query= BRENDA::A0A140N9B6
         (406 letters)



>FitnessBrowser__SB2B:6938533
          Length = 425

 Score =  216 bits (550), Expect = 1e-60
 Identities = 140/402 (34%), Positives = 210/402 (52%), Gaps = 31/402 (7%)

Query: 22  PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN---GY 78
           P    R E + +WD +G+EYIDFAGGIAV   GH HP+++ A+ EQ  KF HT     GY
Sbjct: 25  PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGY 84

Query: 79  TNE-PVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137
            +   V     +L+   FA +     SG+EA E A+K+AR +      + ++G++AF + 
Sbjct: 85  ESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAY------TKRAGVIAFTSG 138

Query: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHA----AYNDINSASALID----------- 181
           +HGRT+  ++  G+ A YS+    + A++  A    A + ++   A+             
Sbjct: 139 YHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEP 198

Query: 182 DSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHY 241
               A+I+EP+QGEGG   A+  F++ LRELC+R   +LI DEVQTG GRTG  +A    
Sbjct: 199 SDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQM 258

Query: 242 GVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINT 301
           GV  D+ T AK++ GGFP+  +    E    +  G  G TYGG+PLA A A  V+E+   
Sbjct: 259 GVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIEVFEE 318

Query: 302 PEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL--NADYAGQ-AKQISQEA 358
            ++L             +  +  RY   +EVRGLG +I   L  N   A +   Q+  EA
Sbjct: 319 EKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLTEA 378

Query: 359 AKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAACE 398
              G+++L  G  GNV+R    +   +E++  GL+  A   E
Sbjct: 379 RNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420


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: 447
Number of extensions: 14
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: 425
Length adjustment: 31
Effective length of query: 375
Effective length of database: 394
Effective search space:   147750
Effective search space used:   147750
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