GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2323
          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:

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