GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Xenophilus azovorans DSM 13620

Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_211260275.1 Q392_RS21735 O-succinylhomoserine sulfhydrylase

Query= BRENDA::Q5H4T8
         (397 letters)



>NCBI__GCF_000745855.1:WP_211260275.1
          Length = 403

 Score =  270 bits (690), Expect = 5e-77
 Identities = 154/371 (41%), Positives = 232/371 (62%), Gaps = 15/371 (4%)

Query: 31  STGAVMPPIYATSTYAQS-SPGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGM 89
           +TG V P    + T AQ  S GE  G+ YSRT NPT  ++E+ +AA+EG   A A ASGM
Sbjct: 36  TTGFVQPD---SETSAQRFSSGE--GYTYSRTSNPTVTSFEQRLAAMEGTEAAIATASGM 90

Query: 90  AATST-VMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRA 148
            A    +M LL AG HVV    ++G T  LF +   +  G++ +F   TD   ++AA+R 
Sbjct: 91  GAILLMIMGLLRAGDHVVLSRSMFGSTLNLFAKEFGKF-GVETTFCSQTDVDEWRAAVRP 149

Query: 149 DTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSA 208
           +TK+++ ETPTNP+ ++ DIAA+A IAR  G L  VDN FA+P+LQRP  LGAD+V+HS 
Sbjct: 150 NTKLLFAETPTNPLTEVCDIAALADIARAAGALLAVDNAFATPILQRPTQLGADIVMHSG 209

Query: 209 TKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAH 268
           TKYL+G   ++ G A+   +  +  + A +  + G V  PF++++ L+GL+TL +R++A 
Sbjct: 210 TKYLDGQGRVMAG-ALCASHELITSKFAPIVRTAGMVLSPFNAWVVLKGLETLGIRVKAQ 268

Query: 269 CENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF-GGIVSIVLKGGFDAAKR- 326
           CE+ LA+A+WLE  P + +V YPGL SHPQH LA RQ +G  GG++S  L G    A R 
Sbjct: 269 CESTLAIARWLEAQPQVARVYYPGLPSHPQHELAMRQQNGLGGGVLSFQLAGDTPEAARA 328

Query: 327 ----FCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDL 382
                 +   L ++A +LG  +++++HPA  +H  +   +R+  GI+   +R++VG+E +
Sbjct: 329 KAFHVIDSCRLLSIATNLGDTKTIISHPASTSHGRLSEEQRQAAGITQGTIRVAVGLEHI 388

Query: 383 GDLRGDLERAL 393
            D++ DL R L
Sbjct: 389 EDIQDDLLRGL 399


Lambda     K      H
   0.320    0.134    0.391 

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: 381
Number of extensions: 18
Number of successful extensions: 5
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: 397
Length of database: 403
Length adjustment: 31
Effective length of query: 366
Effective length of database: 372
Effective search space:   136152
Effective search space used:   136152
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 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