GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Echinicola vietnamensis KMM 6221, DSM 17526

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Cola:Echvi_2283
          Length = 391

 Score =  381 bits (979), Expect = e-110
 Identities = 184/382 (48%), Positives = 258/382 (67%)

Query: 19  FDTLAVRAGQRRTPEGEHGEALFTTSSYVFRTAADAAARFAGEVPGNVYSRYTNPTVRTF 78
           F+T AVR    ++ + EH   ++ TSS+ F +A +A   FA E+PGN+YSRY NP     
Sbjct: 6   FETEAVRIASSKSNQREHSAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDL 65

Query: 79  EERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYFKRFGI 138
            E++ A+EG E  +ATASGM+A+   + SL   GDH+L SRS+FGST  L  + F ++GI
Sbjct: 66  IEKVCAVEGTEDGIATASGMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGI 125

Query: 139 QVDYPPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALLAVDNCFC 198
              Y  +SD+  W+   KPNTK+ F+E+PSNP  E++D+  + + A A   +L VDNCF 
Sbjct: 126 TSTYGDISDIENWDKLVKPNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFA 185

Query: 199 TPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTAGPTLSPFNA 258
           TP LQQP K GAD+V HSATKYIDGQGR +GG++ G+ E +KEV  F R  GP++SPFNA
Sbjct: 186 TPYLQQPAKWGADIVAHSATKYIDGQGRVLGGLILGKQELIKEVQFFTRHTGPSISPFNA 245

Query: 259 WLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELARRQQSGFGA 318
           W+  + +ETL IRM+ H A+ALA+A + +    +E V Y  L SHPQH+LA++Q    G 
Sbjct: 246 WILSRSMETLAIRMERHCANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGG 305

Query: 319 VVSFDVKGGRDAAWRFIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPEDRARAGIGDS 378
           +V+  +KGG + A RFID  +M+++T NLGDT++ I HPA+T+H +L+ E+R R GI   
Sbjct: 306 IVTLTLKGGIERAQRFIDELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPG 365

Query: 379 LIRVAVGLEDLDDLKADMARGL 400
           LIR++ GLE  DD+ AD+ R L
Sbjct: 366 LIRLSAGLEHHDDIIADIERAL 387


Lambda     K      H
   0.319    0.133    0.392 

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: 360
Number of extensions: 10
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: 403
Length of database: 391
Length adjustment: 31
Effective length of query: 372
Effective length of database: 360
Effective search space:   133920
Effective search space used:   133920
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