GapMind for Amino acid biosynthesis

 

Aligments for a candidate for metB in Phaeobacter inhibens BS107

Align Cystathionine gamma-synthase 1, chloroplastic; AtCGS1; METHIONINE OVERACCUMULATION 1; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate GFF2323 PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ

Query= SwissProt::P55217
         (563 letters)



>lcl|FitnessBrowser__Phaeo:GFF2323 PGA1_c23540 O-succinylhomoserine
           sulfhydrylase MetZ
          Length = 396

 Score =  243 bits (620), Expect = 1e-68
 Identities = 140/385 (36%), Positives = 217/385 (56%), Gaps = 9/385 (2%)

Query: 180 VHAGERLGRGIVTDAITTPVVNTSAYFFKKTAELID--FKEKRSVSFEYGRYGNPTTVVL 237
           VH G R  +    + ++  +  T  + +  TAE  +  F E     F Y RYGNPT  + 
Sbjct: 12  VHGGTRRSQ---YNEVSEAIYLTQGFVYD-TAEQAEARFIETGPDEFIYARYGNPTVAMF 67

Query: 238 EDKISALEGAESTLVMASGMCASTVMLLALVPAGGHIVTTTDCYRKTRIFMENFLPKLGI 297
           E++I+ALEGAE     ASGM A    L +++ AG H+V+    +      +EN L + G+
Sbjct: 68  EERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILENILTRYGV 127

Query: 298 TVTVIDPADIAGLEAAVNEFKVSLFFTESPTNPFLRCVDIELVSKICHKRGTLVCIDGTF 357
            VT +D  D+    AA+     ++FF ES +NP L  +DI  V+++ H  G  V +D  F
Sbjct: 128 EVTFVDGTDLDAWRAALRPDTKAVFF-ESMSNPTLEVIDIAAVAELAHAVGATVVVDNVF 186

Query: 358 ATPLNQKALALGADLVVHSATKYIGGHNDVLAGCICGSLKLV-SEIRNLHHVLGGTLNPN 416
           +TP+   A+  GAD+V++SATK+I G   VL G I G+   +   +       GG+L+P 
Sbjct: 187 STPVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHTGGSLSPF 246

Query: 417 AAYLIIRGMKTLHLRVQQQNSTAFRMAEILEAHPKVSHVYYPGLPSHPEHELAKRQMTGF 476
            A+ +++G++T+ LRV  Q  TA  +A+ L  HP +S + YPGL  H +H L +RQ+ G 
Sbjct: 247 NAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALVQRQLGGK 306

Query: 477 GG-VVSFEIDGDIETTIKFVDSLKIPYIAPSFGGCESIVDQPAIMSYWDLPQEERLKYGI 535
           GG V+S ++ G  +   +F+++L IP I+ + G  +SI   PA  ++  L +E + + GI
Sbjct: 307 GGTVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEELKSELGI 366

Query: 536 KDNLVRFSFGVEDFEDVKADILQAL 560
              LVRFS G+ED  D+ AD+ QAL
Sbjct: 367 TPGLVRFSVGLEDAGDLIADLTQAL 391


Lambda     K      H
   0.318    0.132    0.379 

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: 419
Number of extensions: 13
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: 563
Length of database: 396
Length adjustment: 33
Effective length of query: 530
Effective length of database: 363
Effective search space:   192390
Effective search space used:   192390
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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