GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Burkholderia phytofirmans PsJN

Align Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate BPHYT_RS13720 BPHYT_RS13720 O-acetylhomoserine aminocarboxypropyltransferase

Query= SwissProt::P53780
         (464 letters)



>FitnessBrowser__BFirm:BPHYT_RS13720
          Length = 450

 Score =  200 bits (508), Expect = 9e-56
 Identities = 137/401 (34%), Positives = 196/401 (48%), Gaps = 43/401 (10%)

Query: 103 AMSTPLYQTATFKQPSA--------IENGPYDYTRSGNPTRDALESLLAKLDKADRAFCF 154
           A +TP+YQT +F    +        +E   + Y+R  NPT    E  +A L+    A   
Sbjct: 23  ARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAVFEERVAALENGAGAIGT 82

Query: 155 TSGMAALS-AVTHLIKNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTKLDEVAAA 213
            SG AAL  A+  L+  G  IVA   +YGGS  LL   + R G+    V    LD   AA
Sbjct: 83  ASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFGIETTFVKPGDLDAWRAA 142

Query: 214 IGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGADIVM 273
           + P T+L++ E+  NP   + DI  ++++AH     +LVD++  +P L +P E GAD V 
Sbjct: 143 LRPNTRLLFGETLGNPGLDVLDIAAVAQIAHEHRVPLLVDSTFTTPYLLKPFEHGADFVY 202

Query: 274 HSATKFIAGHSDVMAGVLAVKG----EKLAKEVYFLQN---------SEGSGLAPF---- 316
           HSATKF+ GH   + GVL   G    E   +   F +          SE S +APF    
Sbjct: 203 HSATKFLGGHGTTIGGVLVDGGTFDFEASGRFPEFTEPYDGFHGMVFSEESTVAPFLLRA 262

Query: 317 ---------------DCWLCLRGIKTMALRIEKQQENARKIAMYLSSHPRVKKVYYAGLP 361
                            W  L+GI+T+ LR+E+   N R++  +L++H  V+ V Y  LP
Sbjct: 263 RREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVVEFLAAHAAVESVAYPELP 322

Query: 362 DHPGHHL-HFSQAKGAGSVFSF-ITGSVALSKHLVETTKYFSIAVSFGSVKSLISMPCFM 419
            HP H L      +GAG+VFSF + G  A  +  +E    FS   + G  +SL+  P   
Sbjct: 323 THPDHALAKRLLPRGAGAVFSFNLRGDRAAGRSFIEALSLFSHLANVGDARSLVIHPAST 382

Query: 420 SHASIPAEVREARGLTEDLVRISAGIEDVDDLISDLDIAFK 460
           +H  + A    A G+ E  +R+S G+ED DDLI DL  A K
Sbjct: 383 THFRMDAAALAAAGIAEGTIRLSIGLEDPDDLIDDLKRALK 423


Lambda     K      H
   0.316    0.130    0.369 

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: 408
Number of extensions: 27
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: 464
Length of database: 450
Length adjustment: 33
Effective length of query: 431
Effective length of database: 417
Effective search space:   179727
Effective search space used:   179727
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 (21.6 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