GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metZ in Cupriavidus basilensis 4G11

Align O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized)
to candidate RR42_RS31610 RR42_RS31610 cystathionine beta-lyase

Query= SwissProt::P55218
         (403 letters)



>FitnessBrowser__Cup4G11:RR42_RS31610
          Length = 402

 Score =  191 bits (485), Expect = 3e-53
 Identities = 137/393 (34%), Positives = 204/393 (51%), Gaps = 19/393 (4%)

Query: 20  DTLAVRAGQRRTPEGEHGEA---LFTTSSYVFRTAA---DAAARFAGEVPGNVYSRYTNP 73
           DT  + AG     +G HG     +  TS+  F  +    D  AR A     + Y R+   
Sbjct: 6   DTQLIHAGTPPFVQG-HGPVNVPVVRTSTVRFENSDAYDDIRARHARGERVSSYGRHGMD 64

Query: 74  TVRTFEERIAALEGAEQAVATASGMSAILALVMSLCSSGDHVLVSRSVFGSTISLFDKYF 133
           T R  E+ IA LEG  +A    SG++AI    ++L S GDH LV  SV+     L     
Sbjct: 65  THRALEDAIAGLEGGNRAFLAPSGLAAISLTFLALLSPGDHALVVDSVYAPVRRLEQTLL 124

Query: 134 KRFGIQVDY--PPLSDLAAWEAACKPNTKLFFVESPSNPLAELVDIAALAEIAHAKGALL 191
           +R GI+V Y  P   DL   +A  +PNT+L ++ESPS+ L E++D+  L +IAH  G ++
Sbjct: 125 RRLGIEVSYFSPSQDDL---DALIRPNTRLLYLESPSSLLYEVLDLPRLVQIAHRHGVVV 181

Query: 192 AVDNCFCTPALQQPLKLGADVVIHSATKYIDGQGRGMGGVVAGRGEQMKEVVGFLRTA-G 250
           A DN + +    QPL LG D+ I ++TKYI G    M G V  + E +   +       G
Sbjct: 182 ATDNTWASGHALQPLALGVDISILASTKYISGHSDLMQGAVVVKDEALARRIADAHDGFG 241

Query: 251 PTLSPFNAWLFLKGLETLRIRMQAHSASALALAEWLERQPGIERVYYAGLPSHPQHELAR 310
             +S  +A+L L+G+ TL +R+  H  +ALA+A++LE    + RV+Y  LPS P H L  
Sbjct: 242 LAISADDAYLALRGIRTLAVRLAQHQRNALAVAQFLEAHEAVGRVFYPALPSDPGHALWL 301

Query: 311 RQQSGFGAVVSFDVKGGRDAAWR-FIDATRMVSITTNLGDTKTTIAHPATTSHGRLSPED 369
           R  SG   +VSF +     AA R  +D+  +  +  + G  ++ +   A     RL+   
Sbjct: 302 RDFSGANGLVSFSLPTADVAAARKLVDSLSLFGLGASWGGYESLVQVAAPE---RLAEHS 358

Query: 370 RARAGIGDSLIRVAVGLEDLDDLKADMARGLAA 402
             R    + +IR+ +GLE  +DL AD+A+GLAA
Sbjct: 359 YWRG--AEPVIRLHIGLEAPEDLIADLAQGLAA 389


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: 380
Number of extensions: 24
Number of successful extensions: 4
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: 402
Length adjustment: 31
Effective length of query: 372
Effective length of database: 371
Effective search space:   138012
Effective search space used:   138012
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