GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Desulfovibrio vulgaris Miyazaki F

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)

Query= curated2:Q8ZV07
         (383 letters)



>FitnessBrowser__Miya:8499751
          Length = 459

 Score =  132 bits (331), Expect = 3e-35
 Identities = 126/425 (29%), Positives = 198/425 (46%), Gaps = 66/425 (15%)

Query: 15  IVKGFMQYVWDDKGQRYIDCNTNHGV--VFLGHANPKIVEAVKKQVEEIWAVPLNFATPA 72
           +V+G    + D  G+ Y+D  T+ GV  V +G+   +I  AV +Q++   A+P   AT  
Sbjct: 38  VVEGEGLTLRDINGKEYLDA-TSGGVWCVNVGYGRERIARAVYEQMK---AMPYYAATAG 93

Query: 73  RERFIEEFSKLLPPKFGVV--FLQNTGTEAVEVAIKIAKKVTR------KPTIVAFTNSF 124
              +IE   KLL    G+   +L N+G+EA E A K+ + +        K  I+     +
Sbjct: 94  NIPYIEFAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKILFRARDY 153

Query: 125 HGRTMGSLSITWNEKYKKAFEPL------YPHV-----RFGK------FNVPHEVDKLI- 166
           HG T+G+LS T   + K+ F PL      +PH       F K       +    V+++I 
Sbjct: 154 HGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCARAVERIIE 213

Query: 167 --GEDTCC-VVVEPIQGEGGVNPATPEFLKALREEAQRKGALLIFDEVQTGFGRTGAVWA 223
             G +T   ++VEPI   GGV P   E+   L +  +R G LLI DEV  G GRTG ++ 
Sbjct: 214 QEGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCGMGRTGTMFG 273

Query: 224 FQKYGVEPDIFTAGKPVAGG-LPIGLAVAREDFGDVF--EPGEHG------STFAGNAVV 274
           +Q YGV PDI T  K VA   +PI +    E+    F  +P +        ST+ G A  
Sbjct: 274 YQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYFRDISTYGGCAAG 333

Query: 275 MAAAAAASRLLREEDVPGRAERIGAELAKALGDTGSRLAV-RVKGMGLMLGLEL------ 327
            +AA     ++ EE +      +G  L   L + G    V  V+G GL+ G+EL      
Sbjct: 334 CSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGDLPYVGDVRGKGLLCGIELVQDKAG 393

Query: 328 --RVKADQFIQPLLERGVMALTAG---------VNTLRFLPPYMISKEDVEVV----HAA 372
              +   + IQ + E    A+  G          N +   P Y++++++++V+     AA
Sbjct: 394 KKPMAEGKVIQVVGEMAANAVLVGRTNRSLPGFNNIINIAPAYVVTRDNIDVILRTLRAA 453

Query: 373 VTEVL 377
           + +VL
Sbjct: 454 LVKVL 458


Lambda     K      H
   0.320    0.138    0.408 

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: 401
Number of extensions: 22
Number of successful extensions: 2
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: 383
Length of database: 459
Length adjustment: 32
Effective length of query: 351
Effective length of database: 427
Effective search space:   149877
Effective search space used:   149877
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