GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Desulfovibrio vulgaris Hildenborough

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 208056 DVU2559 adenosylmethionine--8-amino-7-oxononanoate aminotransferase

Query= curated2:Q9YBY6
         (388 letters)



>MicrobesOnline__882:208056
          Length = 542

 Score =  123 bits (309), Expect = 1e-32
 Identities = 124/408 (30%), Positives = 187/408 (45%), Gaps = 57/408 (13%)

Query: 28  DDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFS---TPSLEEALTEFS 84
           D  G +YLD  +       GH +P I EA+ RQ  + VA S+      TPS+E A    +
Sbjct: 97  DTDGNRYLDGVSSLWTNVHGHRHPHIDEAIRRQL-DRVAHSTLLGLGGTPSIELA-ARLT 154

Query: 85  RIAPPWAEEIVFLNTGTEAVEAALKAAWLA--------TGKRGIVALKNSFHGRTLASLS 136
            IAP     + + ++G+ AVEAALK A+            +  ++A  N++HG T+ S+S
Sbjct: 155 AIAPAGLTRVFYSDSGSTAVEAALKIAFQYHRQAPEGDARRTRVMAFSNAYHGDTIGSVS 214

Query: 137 VTWNPRYRRGV--PVLDTRFLSPSTDP-----------------GEVEKLVPE---DTAA 174
           +     +  G+  P+L     +P+                    GEVE+L+     +  A
Sbjct: 215 LGGMSLFH-GIYGPLLFDPVRAPAPHCYRCPADLRPETCGMACLGEVERLMRHHGHELCA 273

Query: 175 IIVEP-IQGEGGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHESLGVEP 233
           ++VEP +QG  G+        + LR+  DR G  ++ DE+  GFG+TG ++A E  GV P
Sbjct: 274 VVVEPLVQGAAGMLVQPRGWLRGLRDLCDRHGVFMVADEVAVGFGKTGTMFACEQEGVVP 333

Query: 234 DIMTAGKSIAGG-LPASAVLSRE----GVLATLASGR---HGSTHAANPLSMAAVAAASR 285
           D++   K I GG LP +A L  E    G L   A  R   HG T+  N L+ AA  A+  
Sbjct: 334 DMLCLAKGITGGYLPLAATLVTEHIHDGFLGGYADFRTFFHGHTYTGNALACAAALASLD 393

Query: 286 FLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVEL------RLDPGPVL 339
              EE   +  R     L  LL   +  L  V  +R  G+M G+EL      R    P  
Sbjct: 394 VFEEERTLETLRPRIERLATLLAP-LNDLPHVGDIRRVGVMTGIELVADRETRTPYRPEE 452

Query: 340 R-----CLQESERVLALRSGATVVRLLPPYSISREDAEMVVYGLERCI 382
           R      L+   R + +R    V+ L+PP SI+  + E +V+ +   I
Sbjct: 453 RIGHRVTLEARRRGVIVRPLGDVMVLMPPLSITETELETLVHTVRGAI 500


Lambda     K      H
   0.319    0.136    0.398 

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: 479
Number of extensions: 29
Number of successful extensions: 1
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: 388
Length of database: 542
Length adjustment: 33
Effective length of query: 355
Effective length of database: 509
Effective search space:   180695
Effective search space used:   180695
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: 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