GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Stenotrophomonas chelatiphaga DSM 21508

Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_057509267.1 ABB28_RS14300 M20 family metallopeptidase

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_001431535.1:WP_057509267.1
          Length = 439

 Score =  255 bits (651), Expect = 2e-72
 Identities = 153/401 (38%), Positives = 217/401 (54%), Gaps = 22/401 (5%)

Query: 12  ASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAF 71
           A + + QVV WRR  H HPELS  E+ TSA +   L  +G+  K  +  + V+  I+G  
Sbjct: 33  AQRLQAQVVEWRRDFHQHPELSNREERTSAEVAKRLRAMGLKPKTGIAHHGVVAIIEGGK 92

Query: 72  DGPVVGLRADMDALPITEVTGLPFTS--------ENPGVMHACGHDSHMAILLGAAAILQ 123
            GP + LRADMDALP+TE TGLPF S        +  GVMHACGHD+H A LLG A  L 
Sbjct: 93  PGPKIALRADMDALPVTEQTGLPFASKATSTYRGQQVGVMHACGHDAHTATLLGVAEALV 152

Query: 124 SVKDQLHGTVKLVIQPAEEEALIK---GAQGIVDSGVLDDV--DEIYGLHVWPQLPVGTV 178
           +++  L G V L+ QPAEE A      GA  ++  GV  D   + ++GLHV+  +  G +
Sbjct: 153 AMRKDLPGQVMLIFQPAEEGAPSPEEGGAALMLKEGVFADFKPEAVFGLHVFSSVQAGKI 212

Query: 179 GLKKGNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETN-PMDNL 237
            ++ G LMAASDRF + + G+ THG+ P NG+D IVA A+ I   +++V+R TN      
Sbjct: 213 AVRGGPLMAASDRFGIKVIGRQTHGSAPWNGVDPIVATADLIGTAQTIVSRRTNLAQQPA 272

Query: 238 VCTIGVFNSGDRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEY 297
           V T G  N G RYN+   +  + GT RT+D   R  I   L    +      G T+  E 
Sbjct: 273 VVTFGAINGGIRYNIIPDEVEMVGTIRTFDEGMRQQIFADLRNVAEHTTAAHGATAVTEI 332

Query: 298 --RRGHGATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLG 355
               G+ AT+ND      +   ++  +GKD V  P    M AEDFS +  ++ G F ++G
Sbjct: 333 YEAEGNPATVNDPQLTARMLPSLQAVVGKDNVYEPPL-QMGAEDFSLFAREVPGMFFFVG 391

Query: 356 TGFEG-----NPALHNAAFTIDESILEPGITMMAGIAAELL 391
           +  EG      PA H+  F +DE  L+ G+  +  ++ + L
Sbjct: 392 STSEGIDPAKAPANHSPKFLLDEKALDVGLRALLQVSLDYL 432


Lambda     K      H
   0.318    0.136    0.401 

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: 452
Number of extensions: 18
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: 394
Length of database: 439
Length adjustment: 31
Effective length of query: 363
Effective length of database: 408
Effective search space:   148104
Effective search space used:   148104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 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