GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Pontibacter ramchanderi LP43

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_101445362.1 BD749_RS13990 aspartate aminotransferase family protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_002846395.1:WP_101445362.1
          Length = 396

 Score =  204 bits (519), Expect = 4e-57
 Identities = 126/373 (33%), Positives = 203/373 (54%), Gaps = 29/373 (7%)

Query: 27  RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH--TGNGYTNEPVL 84
           + EG  ++   G  YID   GI V+ +GH HP++++A+ +Q  ++ H      +   P  
Sbjct: 26  KAEGIYMYGSDGHRYIDLISGIGVSNVGHRHPKVLRAIHDQLDRYMHLMVYGEFVQGPQA 85

Query: 85  RLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRT 142
           +LA+ L        + V+  NSG EA E A+KLA++Y      + ++G V  +NA+HG T
Sbjct: 86  QLAQALCSTLPPRLNNVYLLNSGTEAVEGAMKLAKRY------TGRTGFVTCRNAYHGST 139

Query: 143 LFTVSAGGQPAYSQDFAPLPPQIQ---HAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVV 199
              +S  G   +   F PL P ++   H    DL      I ++T A+I+E +QGE G+ 
Sbjct: 140 QGALSVNGSEGFKNAFRPLLPDVRVINHGAIPDLQQ----ITEHTAAIIIEAVQGEAGLR 195

Query: 200 PADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFP 259
             +A +++ LR+ C    ALLI DE+QTG GRTG  +A+  +G+ PD+L  AK +GGG P
Sbjct: 196 VPEASYMQALRDRCTEVGALLILDEIQTGFGRTGTFWAFEQFGIEPDILLCAKGMGGGMP 255

Query: 260 IGALLASERCASVM---TVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFC 316
           IGA +A +   +V     +  H TT+GG+P++CA +     TI    +L GV+++   F 
Sbjct: 256 IGAFIAPQEIMAVFKNDPILGHLTTFGGHPVSCAASLATLQTIQEENLLAGVEEKANLFR 315

Query: 317 ERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMI--LIAGANVVR 374
           E L  ++ R    K IR  GL++    + E     KA+ +QA   G++    +   N +R
Sbjct: 316 ELL--VHPR---IKGIRNKGLMMAA--EFESFEVLKAVIDQAIVNGVLTDWFLFCDNSMR 368

Query: 375 FAPALIISEDEVN 387
            AP LII+E++++
Sbjct: 369 IAPPLIITEEQIH 381


Lambda     K      H
   0.321    0.137    0.412 

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: 414
Number of extensions: 28
Number of successful extensions: 6
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: 396
Length adjustment: 31
Effective length of query: 375
Effective length of database: 365
Effective search space:   136875
Effective search space used:   136875
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 Jul 26 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